Micro RNAs(mi RNAs) are ~21 nucleotide(nt), endogenous RNAs that regulate gene expression in plants. Increasing evidence suggests that mi RNAs play an important role in species-specific development in plants. However, the detailed mi RNA profile divergence has not been performed among tomato species. In this study, the small RNA(s RNA) profiles of Solanum lycopersicum cultivar 9706 and Solanum habrochaites species PI 134417 were obtained by deep sequencing. Sixty-three known mi RNA families were identified from these two species, of which 39 were common. Further mi RNA profile comparison showed that 24 known non-conserved mi RNA families were species-specific between these two tomato species. In addition, six conserved mi RNA families displayed an apparent divergent expression pattern between the two tomato species. Our results suggested that species-specific, non-conserved mi RNAs and divergent expression of conserved mi RNAs might contribute to developmental changes and phenotypic variation between the two tomato species. Twenty new mi RNAs were also identified in S. lycopersicum. This research significantly increases the number of known mi RNA families in tomato and provides the first set of small RNAs in S. habrochaites. It also suggests that mi RNAs have an important role in species-specific plant developmental regulation. MicroRNAs (mi RNAs) are ~ 21 nucleotide (nt), endogenous RNAs that regulate gene expression in plants. Increasing evidence suggests that mi RNAs play an important role in species-specific development in plants. However, the detailed mi RNA profile divergence has Three of the miRNA families identified were identified from these two species, and were found in tomato species. In this study, the small RNA (s RNA) profiles of Solanum lycopersicum cultivar 9706 and Solanum habrochaites species PI 134417 were obtained by deep sequencing. of which 39 were common. Further mi RNA profiles comparison that 24 known non-conserved mi RNA families were species-specific between these two tomato species. In addition, six conserved miRNA families displayed an apparent divergent expression pattern between the two tomato species . Our results suggested that species-specific, non-conserved mi RNAs and divergent expression of conserved mi RNAs might contribute to developmental changes and phenotypic va Ration between the two tomato species. Twenty new mi RNAs were also identified in S. lycopersicum. This research significantly increases the number of known mi RNA families in tomato and provide the first set of small RNAs in S. habrochaites. It also suggests that mi RNAs have an important role in species-specific plant developmental regulation.