The greater short-nosed fruit bat (Cynopterus sphinx) is a social species, widely distributed in southern Asia. We used microsatellite and mfDNA markers to assess whether this fruit bat has a sex biased dispersal pattern. We also assessed signatures of sex-biased migration using microsatellite data. No significant heterozygosity deficiency (F_IS), lower assignment value (mAIc) and variance of assignment (vAIc) were found between females and males, which does not support the hypothesis that dispersal in C. sphinx is sex biased. When microsatellite genotype frequency and mfDNA haplotype distribution patterns were subjected to the AMOVA, we found that genetic partitioning was higher at mfDNA (Φ_ST) than autosomal markers (F_ST) in both sexes. There is a higher value for males than females in both the mtDNA and microsatellite data, and both adult males and females also exhibited more variation within than among populations, but without significant results. Our results indicated that C. sphinx displayed various sexual population structures and there is no sex-biased dispersal, which is in accordance with concomitant ecological studies.