Well, there are a few reasons why they are less corrupt, although this is a topic definitely worthy of more academic attention. Both countries have quite small populations. I know more about Botswana though so will focus on that. Botswana had several things going for it: colonial incursion compared to other parts of British colonial Africa were minimal. Diamonds and other precious minerals were not found in any substantial degree until after WWII. It was also set up by the British in the nineteenth century as a special protectorate where white settlement was banned, so neither colonial settlers nor colonial economic exploitation ever really took hold in the ways it did in other parts of the world. In other words, Botswana was an insignificant and neglected backwater (from a colonial perspective), which meant at indepedence it was one of the poorest places in the world.

I'm simplifying somewhat but basically around the time if independence, diamonds and other precious mineral were discovered. They ended up with elected officials who were largely very successful at investing these resources in education and developing other aspects of a state infrastructure. The relatively small and homogenous size of the population made this easier. It is difficult to read about Seretse Khama's lengthy presidency and not want to celebrate his achievements in assuring Botswana managed the transition to successful liberal democracy with some ease and has not shared the violence of many of its neighbours.

I now want to make a major caviat about everything I've just written. It's too simplistic. While this is the general narrative, it's worth bearing in mind that the nomad people of the Kalahari Desert were largely marginalised in both Namibia and Botswana (traditionally their residence spanned both), denied access to education and generally have faced discrimination. Botswana recently has suffered, like most of southern Africa, from incredibly high rates of HIV - perhaps up to 25% of the population.

In addition to this, some of the image of success may also be down to a lack of research compared to other parts of Africa. In Botswana, historians have largely focused on WWII, the love story of Seretse Khama and Ruth Williams in Botswana, and the shenanigans of the US and South Africa and Britain interferring because of uranium in the 1950s and 1960s. And just fundamentally, it's nice to think that African countries don't have to be basket cases, that a success like Botswana is possible. Botswanans themselves take a lot of pride in this image of their country, which probably further helps keep corruption down and retain peace.

Anyway, that's a slightly simple summary but I hope answers your question. If you want to read about it, I've just bought myself a book that looks quite interesting (although I haven't had time to read it yet): Ellen Hillbom and Jutta Bolt's Botswana – A Modern Economic History: An African Diamond in the Rough (2018), although there are plenty of older good books on the topic.

The puzzle of Africa’s underdevelopment has been a Pandora’s box for comparitivists as they conceptualize the post-colonial epoch. How can a region so rich in natural resources contain such a disproportionate amount of the world’s poor countries? This phenomenon within the developing world has been dubbed ‘the resource curse.’ Natural resources were once heralded as the developing worlds’ ticket to the party—now the contemporary view of natural resources is far more trepidatious. Natural resources are now often associated with corruption, conflict, and inequality in developing countries. While the presence of natural resources within a country can be harmful towards development, the outcome need not be so assured. With proper management and accountability of the resource sector, a country can see real development outcomes while avoiding the pitfalls of the ‘curse.’ Indeed, the contemporary view of the resource curse has increasingly been to focus less on the resources and more on who is controlling them. The political institutions of resource exporting countries are paramount in achieving long term economic development. With this in mind, the political landscape of Africa does itself no favors in alleviating the resource curse. The continent is rife with strong-men dictators serving as Presidents in quasi-democracies. Crucially and paradoxically absent are the institutions in place to curb executive power in African Presidential systems.

Africa’s disproportionate amount of failing Presidential democracies informed the hypothesis that the typology of democratic regime in Africa is crucial in its ability to deal with the resource curse effectively. Despite the negative associations of the resource curse, Botswana has been the shining example of an African state that has been able to effectively achieve long term development goals on the back of economic growth caused by resource exportation. It is my view that it is not a coincidence that Botswana is one of the few examples of a Parliamentary Republic in Africa. The facets of Botswana’s Parliamentary institutions which allow for the country to deal with the resource curse more effectively than a Presidential system will be discussed at length.

It must be reiterated that Africa is a region that—for economic and sociohistorical reasons--trends towards the centralization of power. Paradoxically, the political system that theoretically is best equip to deal with this through checks and balances has had the opposite effect. The resource rich nations of Africa have seen their riches plundered by corrupt presidential administrations that have actively worked to weaken the political institutions around them to remain in power for personal profit.Going further SMDP voting systems foster the two-way relationship between voter and representative that is a backbone of liberal democracy. SMDP systems are required to develop local institutions and ensure individual representatives are accountable to the voters and not the government that put them in power. Thus, the combination of parliamentarism and SMDP combine for an environment that is most conducive to the type of accountable policy making required to alleviate the resource curse.

Although on the surface Africa, ethnically and culturally diverse as it is, seems to be an ideal candidate for proportional representation (PR) voting systems, but when put into practice there is little evidence that PR systems do more to represent minority groups than SMDP. Much in the same token as other political paradoxes in the continent, PR systems often have the opposite of their intended effect in Africa. The fragmentation of political parties caused by PR sometimes serves only to disenfranchise minorities more as they are not able to organize into a political opposition large enough to be taken seriously. PR systems are presupposed on a level of party institutionalization that doesn’t exist in Africa.

Continued..

I'm going to offer a really different take on Botswana here that is historical in a different sense.

One of the things that kind of drives me nuts about comparative political science and comparative development economics is that they don't really treat historical change as a complex system in the formal sense of that term. Complex systems involve the simultaneous interaction of numerous actors and actions; these can give rise to new structures or forms that are what might be called "emergent"--not planned, not controlled, and you can't relate the new state back to some single variable that can be selected out through regressions, or even several variables.

So some scholars look at Botswana and they say, "What's the magic ingredient? One dominant ethnicity? A small territory? Relatively low population density? Diamonds? Proximity to a major industrial state?" They're looking for a variable you could swap in to other situations and get the same result.

I'm going to suggest instead that Botswana's postcolonial state--low corruption, multiparty democracy, etc.-- is the result of a whole series of small simultaneities that can't be reproduced or recreated easily. This is not to say that you can't take note of some important causal factors, but it is to say that they're not things you can isolate from their context and compare in the style of social science.

You have to look first at the extent to which Setswana-speakers in the 18th Century had some roughly or crudely democratic norms around deliberation in community. You have to look second at the kinds of small states that Tswana rulers were forming in the 18th and early 19th Century, and then look especially at Khama III (aka Khama 'the Great') who made some distinctive moves in trying to consolidate an unusually large and more centralized kingdom under disputed circumstances. He didn't make military moves; instead he looked to use mission Christianity, recently encountered, to his own advantage and to create new kinds of political personhood with new opportunities in his new state. Or perhaps you could say that some of his subjects, particularly women, made that move and he simply recognized its possibilities. (This is all described very well in Paul Landau, The Realm of the World, and also in Jean Comaroff and John Comaroff, Revelation and Revolution.)

This is not that dissimilar to what other rulers in the region attempted, and it's why I say this isn't a single variable you can just extract from context and apply elsewhere. It didn't work the same way for Moshweshwe's Basotho kingdom because to some extent he had the bad luck to be in the wrong location, but also because he didn't quite make the same subtle moves that Khama and some of his subjects made. Among them, Khama stayed in control of the missionaries rather than the other way around.

This led to various Tswana rulers negotiating with the British for slightly different and slightly more favorable terms of incorporation in the British Empire. Which led to slightly more breathing room and autonomy for later Tswana rulers like Tshekedi Khama vis-a-vis imperial authority. (Well described in Michael Crowder's Flogging of Phineas Macintosh.) Which led, among other things, to Seretse Khama being educated in London and marrying Ruth Williams and approaching the transition to independence in a dramatically different way than many of his neighboring nationalist peers. Which led to some extent to a different sort of cultural and institutional respect for multipartyism and government probity. Which paid off because of diamonds, because of low population density, because the country is small, because it is close to South Africa, etc.

The point being that Botswana has many things in common with its neighbors, but that the culture of its government has been subtly inflected in a different direction from a very early date in ways that can't be easily reproduced, that aren't a magic recipe, but that are meaningful explanations of difference nevertheless. This sort of argument disappoints most development economists and political scientists, who want a magic recipe. History offers different lessons, at least some of the time, about why there are differences when otherwise things look as if they should be the same.