The origin and affiliation of Indian Jewish groups with other world populations remain a point of contention due to a lack of written records or inscriptions. Previous genetic investigations have discovered indications of Indian Jewish and Middle Eastern (Jewish) communities sharing a modest heritage. However, these studies (which rely on a small number of people) haven’t looked into the historical and spatial hybridization of Indian Jewish groups with local Indian populations in detail. We rebuilt Indian Jewish genetic history by studying patterns of genetic variation using a large sample size and a mix of high-resolution biparental (autosomal) and uniparental (Y chromosome and mitochondrial DNA) markers. We found a modest Middle Eastern specific ancestry component among Indian Jewish groups, but it was almost non-existent among their local Indian neighbors, confirming prior findings. The earliest admixture of migrant Jewish communities from the Middle East to South India (Cochin) occurred during the fifth century, according to the temporal test of admixture. Overall, we found that Jewish mixing and migration in India left a trace in their genomes that may be used to connect them to the ‘Jewish Diaspora.’