Scientific racism did not actually begin in the 19th century, but it did change character and gain a new momentum after about the second decade of the 19th century. As the institution of slavery came under increased attack in Europe and in the U.S., apologists for the 'peculiar institution' began to seek support for its justification in new pseudo-scientific theories about race. One of the signifying factors of 19th century scientific racism is evident in the rise of quantification as a way of scientizing what were really folk beliefs about racial differences. In particular, the work of Samuel G. Morton, Paul Broca, and others convinced many that the races of man (the number of these races ranged anywhere from four to around two dozen, depending on who you asked) could be arranged in hierarchies of intelligence and other areas of aptitude, always with Africans at the bottom and Caucasians at the top. Some theorists in the U.S., such as Josiah Clark Nott and Louis Agassiz, went so far as to claim that morphological differences between the races -- apparently supported by statistical biometric data -- indicated that the races of man were in fact separate species with unique origins. This theory, known as polygenesis or polygenism, did not originate in the 19th century. A number of racial theorists in the 18th century had speculated on this idea, though no one at the time could offer what seemed like a firm basis for the claim. But the idea gained new traction with the rise of a new ethnology based on quantification.

Interestingly, the popularity of polygenisis as an explanation for racial differences was also a result of a concurrent decline in the authority of the Bible on the question of human origins. There is much to say about this, but in short, the rise of geology and our first realizations about 'deep time' encouraged naturalists to think beyond the mosaic account of human history.

Other 19th century trends in scientific racism -- notably theories and policies relating to eugenics, the heritability of intelligence, etc. -- came about later in the century as a result of speculation on the implications of Darwinism for the human race. Much of this originated ironically with Darwin's cousin Francis Galton, who also coined the term 'eugenics.'

Ive written a bit about 19th century phrenology and scientific racism, but Im unsure as to exactly what you are asking. Could you rephrase the question, or explain it in more detail?

The origins of 19th century scientific racism are plentiful, and largely lay at the confluence of an increased interest in naturalism (a leftover of the Enlightenment), and the traditional racist and racialist attitudes of European and Americans.