Occurrence and morphometric variation were recorded over one and a half years for two species of frugivorous bats, Cynopterus sphinx and Rousettus leschenaulti, from six localities in and around a tropical rainforest in Xishuangbanna, SW-China. Occurrence of both species was simultaneous. The two species breed all throughout the year, but we found one distinct peak in breeding season for each species. Although the overall morphology between the two species did not differ significantly, statistical analysis of morphological characters revealed consistent spatial correlations for both taxa. Body size and forearm length for both univariate and multivariate analyses (as derived from principal component analysis) was strongly and positively correlated with morphometric variations across the locations for C. sphinx and R. leschenaulti. Both, the different peaks in breeding season and the consistent spatial correlations suggest mechanisms to help resource partitioning. The study represents the first species documentation from this area.