Genetic structure and polygenetic relationship of six numerically larger endogamous tribes, Mina, Bhil, Garasia, Damor and Kathodi of Rajasthan, who exhibit varied ethnographic history, have been investigated using 12 sero-genetic polymorphic marker systems viz. A1A2BO, MNSs, Rhesus, Duffy, Lewis, Kell, Kidd, HP, TF, GPI, G6PD deficiency and HB variants. Genetic differentiation with respect to studied genes has been observed small (except for HB* variants and G6PD*Def, which may be under the influence of natural selection) among the studied tribes and it appears that there has been little effect of population subdivision on these genes or late divergence of these populations from one another. The studied tribes make two main clusters, one of Mina and Saharia, other of Bhil, Damor, Garasia and Kathodi. Within the later cluster Bhil and Damor are closest joined by Garasia and then Kathodi. The present study partially supports the ethnographer’s views of their origin and divergence.