Introduction: Zeme and Kuki tribes are the hill inhabitants of Manipur who belong to TibetoBurman speaking groups. Aim: The present study attempt to assess the extent of heterogeneity of the genetic structure of Zeme and Kuki tribes of Manipur. Methods: Five Alu InDel markers were screened on 188 individuals of two tribal groups of Manipur. Results and Conclusion: All the five loci are found to be polymorphic. Genotype frequencies for all the loci are in reasonable agreement with their respective Hardy-Weinberg proportions except in PV92 among the Kuki tribe. Average heterozygosity levels are high and degree of differentiation is low (Gst-1.7%), revealing that genetic drift is unlikely to play a significant role in the process of genetic differentiation. Genetic distance analysis indicates that Zeme and Kabui, Kuki and Meitei are close to each other. However, the affinities of Kukis with Meitei need further investigation. The genetic structure by and large revealed that the population groups of Manipur are neither overtly admixed nor isolated. Furthermore, the composition of genes in the population groups of Manipur are comparable to each other and that differential heterozygosity might have led to variable influx of genes into these groups, but with similar sources.