It is important to note that the peoples of the Indian subcontinent have never truly regarded themselves as one homogeneous ethnicity. People we refer to as Indian now have historically been: Tamil, Punjabi, Balochi, Bengali, Rajput etc., usually each with their own language, culture and historical kingdom. Think of the term Indian as equivalent of European and each of the aforementioned ethnicities similar to being English or German or French within this analogy. However, sociology in India is even more complicated since you also have the caste system adding another dimension to social structure; people of the same ethnicities may be of different castes. But we are talking about bloodlines, not beliefs - one important point is that religion is one of the few things in India which transcends the boundaries of race and caste.

When Islam was first introduced to the subcontinent it was through traders along the overground trade routes (trans-afghanistan) and indian ocean trade routes (coastal areas of India/Pakistan/Maldives); the first mosque in India (Cheraman Juma Masjid) was built in coastal Kerala in 629 AD, before the first Muslim military incursion into India in 664 AD, led by Abu Said into the northwest of Pakistan (It is also important to note that these places are thousands of miles away and pretty much have nothing to do with each other). We can therefore infer that Islam spread and was converting people already living in the area and from its introduction in the subcontinent. Traders however were more prevalent in some areas than others (Peshawar, Kerala, Bengal, the Maldives) and it was in these areas and amongst these people that Islam really gained a foothold. Islam did not really establish itself away from trade routes or centres of administration; the new religion did not really penetrate the Indian hinterlands or its peoples.

Later when Muslim conquerors arrived, they simply added to the caste and multi-ethnic system of the subcontinent simply by being new categories and made it more advantageous to become Muslim (or in the caste system to be of Persian or Arab origin). Islam gained new converts in areas under Muslim administration.

To answer your question, Hindus and Muslims of the subcontinent will have a shared ancestry amongst some peoples but Islam established itself more firmly with some ethnicities than others. Hinduism and Islam are religions on the subcontinent, not ethnicities. Each have the power to transcend them.

The ancestry of Muslims in the Indian subcontinent is sort of a mixed bag.

Early trade between Arabs and Indians resulted in some native Indians adopting Islam, as well as intermarriage and the subsequent Indo-Arab Muslims (primarily on the west-coast of the Indian peninsula).

Later Arab conquests by the Umayyads penetrated into what is now southern-Pakistan, and resulted in an even greater Indo-Arab mix.

Later still, we have the Turkic-Persian influx into modern-day Pakistan and Western India, via the conquests of the Ghaznavid Empire (later the Delhi Sultanate).

Lastly, we have the emergence of the Mughal Empire, which spanned the entire subcontinent, and introduced a Turkic-Mongol strain to an already hectic ethnic salad bowl.

As you can see, much of the Arab/Persian/Mongol influence is seen in Northwest region of the subcontinent, which not coincidentally, is where most of the Muslims are found (typically with lighter-skin than their non-ethnic Indian counterparts).

There are also however, many subcontinent Muslims who accepted Islam without significant amounts of foreign mixing, and thus are ethnically indistinguishable from their non-Muslim neighbors (Bangladesh is a prime example).

To make matters more complicated, there are various non-Muslim-related ethnic groups within India, which make clean comparisons between Muslims and Hindus/Indians...well, even more complicated.

The religious divide between Hindus and Muslims deserves its own thread, and while ethnic differences certainly played a part in the conflict, there were a host of other factors which when taken in concert, overwhelm any ethnic dimensions that were present.