Bighead carp and silver carp are also the main commercial fishes captured and cultured in China and several other countries. There are, however, some physiological and morphological differences between these two species, such as the huge difference of the size of their skull bones. There has been abundant research into the temperature and salinity tolerance, sexual maturity and mating behavior, spawning, early development and feeding habits of the two carps. Biological processes and physiological differences between these two species are related to changes at the molecular level and probably involve both transcriptional and post-transcriptional regulation of gene expression which are still poorly understood. In this study, we adopted the high-throughput sequencing method to characterize small RNA transcriptomes of bighead and silver carp, analyze their whole microRNA transcriptomes. With this strategy, we identified 167 Nutlin-3 conserved miRNAs in bighead carp and 166 in silver carp, and discovered 39 novel miRNAs in bighead carp and 54 in silver carp. High Throughput Sequencing technologies detect known and novel miRNAs and can also open doors to directly show differences in expression levels. It is widely believed that changes in gene expression patterns underlie many phenotypic differences within, and between, species. In our study, 167 conserved miRNAs were found in bighead carp and 166 in silver carp. Most of these miRNA exist in both carps. The majority of differences were found in the expression level rather than in the sequence conservation of miRNAs. Bighead carp and silver carp exhibit subtle differences in physiology, which is in line with the high number of conserved miRNA expression patterns. A previous study showed that variation in miRNA expression contributes to the differences in physiology, and that the greater the variation in miRNA expression, the larger the differences in physiology. The most striking physiological difference between bighead carp and silver carp is seen in the structure of the head, so we speculate that changes in the miRNA expression might associate with the structure of the head. In our analysis of miRNA expression in the two carps, some conserved miRNAs showed expression differences, which is in agreement with other studies. Therefore, these studies indicate that the correlation between sequence conservation and expression conservation is weak. But, the majority of conserved miRNAs follow a trend of conserved expression between bighead carp and silver carp.