Small isolated populations are a raw material for speciation. Populations that get isolated from the main population are often small and soon begin evolving independently. However, small populations are prone to impacts of drifts and inbreeding which makes them vulnerable to extinction. With whole genome sequences of several endangered populations of tigers and rhinoceros we show that small isolated populations often purge some of their deleterious allele loads. However, whatever deleterious alleles remain in the population, are in high frequency and homozygosity. This might lead the population to extinction. We further observe with simulations and emperical observations that migrations from a different population although increases the deleterious allele load, also lead to decrease in the frequency of deleterious alleles and their homozygosity. Does this indicate that allopatric species also need mild gene flow from other populations?