Hox gene clusters play an important role in the early embryonic development, tissue differentiation and morphogenesis in animals. Megalobrama amblycephala, also known as Wuchang fish, is an economically important freshwater fish and widely distributed in lakes in the middle and lower reaches of the Yangtze River in China.In order to explore the Hox distribution, evolution and expression patterns in M. amblycephala, we conducted a series of analyses based on the whole genome M. amblycephala. In the present study, we identified all the Hox clusters of M. amblycephala from the whole genome data. Combined with the multiple methods, we analyzed chromosome distribution and constructed the Hox phylogenetic tree based on protein sequences. In addition, the expression patterns of Hox in different tissues were further investigated by calculating the number of transcriptional fragments (FPKM).The results showed that 49 Hox genes were identified in the genome of M. amblycephla, and were divided into 7 groups: HoxAa, HoxAb, HoxBa, HoxBb, HoxCa, HoxCb and HoxDa. Transcriptome results indicated that M. amblycephala Hox gene family had different expression patterns. There were significant differences in the expression level of all Hox genes in the muscle of M. amblycephala and Danio rerio, while the expression pattern was similar. In the HoxA cluster, HoxA10b, HoxA3a, HoxA2a and HoxA1a were highly expressed in the muscles of M. amblycephala, and the expression level was higher than that of D. rerio; HoxA13a and HoxA13b are not expressed in the muscle of both of fishes; In the HoxB cluster, HoxB10a, HoxB9a and HoxB7a were highly expressed in muscle tissue of M. amblycephala, while HoxB9a, HoxB8a, HoxB7a and HoxB6a were highly expressed in muscle tissue of D. rerio. In the HoxC cluster, HoxC9a, HoxC2a, HoxC3a and HoxC6b are highly expressed in muscle tissue of M. amblycephala and HoxC8a and HoxC3a are highly expressed in D. rerio, while HoxC13a, HoxC12a, HoxC11a, HoxC4a, HoxC1a, HoxC13b, HoxC12b and HoxC11b are very low or even not expressed in muscle tissue of the two fish species; In the HoxD cluster, HoxD10a, HoxD9a and HoxD3a are highly expressed in muscle tissue of M. amblycephala and HoxD9a is highly expressed in D. rerio, while the expression levels of HoxD13a, HoxD12a and HoxD11a are not expressed in muscle tissue of M. amblycephala and HoxD13a is not expressed in muscle tissue of D. rerio. In addition, comparative transcriptome analysis of three embryonic stages and three tissues of M. amblycephala indicated that HoxA2a, HoxA3a, HoxB9a, HoxB3a, HoxB8a, HoxB1b, HoxB5a, HoxB5b, HoxC3a and HoxC4a were highly expressed at the juvenile fish, while others showed low or even no expression in muscle, intermuscular bone and connective tissues except HoxB7a, HoxB10a and HoxB9a, HoxC3a and HoxC8a. In the HoxD family, HoxD9a, HoxD10a and HoxD11a were expressed in the stage II of embryo. Taken together, these results may lay the foundation for further exploring the function of the Hox gene family of M. amblycephala, and may also provide reference data for other fish Hox studies. In addition, studying the expression patterns of Hox in the formation of intermuscular bone of M. amblycephala also provides reference and theoretical basis for the study of intermuscular bone in other bony fishes.