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MicroRNAs (miRNAs) are ~21 nucleotide (nt), endogenous RNAs that regulate gene expression in plants. Increasing evidence suggests that miRNAs play an important role in species-speciifc development in plants. However, the detailed miRNA proifle divergence has not been performed among tomato species. In this study, the smal RNA (sRNA) proifles of Solanum lycopersicumcultivar 9706 andSolanum habrochaites species PI 134417 were obtained by deep sequencing. Sixty-three known miRNA families were identiifed from these two species, of which 39 were common. Further miRNA proifle comparison showed that 24 known non-conserved miRNA families were species-speciifc 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-speciifc, non-conserved miRNAs and divergent expression of conserved miRNAs might contribute to developmental changes and phenotypic variation between the two tomato species. Twenty new miRNAs were also identiifed inS. lycopersicum. This research signiifcantly increases the number of known miRNA families in tomato and provides the ifrst set of smal RNAs inS. habrochaites. It also suggests that miRNAs have an important role in species-speciifc plant developmental regulation.