Abstract: In order to study the molecular regulation mechanism of the soft intermuscular bones in Rice flower carp, the intermuscular bones of Rice flower carp and Jian carp were collected for high-throughput sequencing of microRNAs (miRNAs) and bioinformatics analysis. 25474895 and 24625715 high quality sequences of 18—32 nt, as well as 595 and 570 known mature miRNAs were obtained from the small RNA library of Rice flower carp and Jian carp intermuscular bone, respectively. Compared with Jian carp, 84 miRNAs were up-regulated and 267 were down-regulated in the intermuscular bone of Rice flower carp. Seven of the down-regulated miRNAs in Rice flower carp were reported as promoting human osteogenesis. Six of the up-regulated miRNAs were reported as inhibit human osteogenesis. These results indicated that Rice flower carp may inhibit the process of osteogenesis by down-regulating the expression of osteogenic miRNAs and up-regulating the expression of osteogenesis inhibiting miRNAs. Therefore it can maintain its intermuscular bone small and soft characteristics. This study laid the groundwork for the study of molecular regulation mechanism of intermuscular bone development.