So far we have no clear understanding on the adipose fin development. In order to find out the differences between the adipose fin and dorsal fin developments, we investigated the developing process and ossification process of dorsal fin and adipose fin in Pristella maxillaris. We found that the dorsal fin bud showed up from the larva fish dorsal at 28 DAH (day after hatch), dorsal fin ray could be seen at 30 DAH, and dorsal fin rays ossified at 35 DAH, whereas, the adipose fin could be found from 32 DAH. Based on this observation, we sequenced the transcriptoms of the dorsal fin bud at 28 DAH, dorsal fin at 30 DAH and adipose fin at 35 DAH in P. maxillaris. A series of bioinformatic analysis showed that all three tissues had 14 115 same genes, accounting for 84.01% of the dorsal fin bud's transcriptome, 83.19% of the dorsal fin's transcriptome, and 84.14% of the adipose fin's transcriptome, indicating that there might be similar molecular mechanism of the development process of adipose fin and dorsal fin in P. maxillaris. At gene expression level, compared with adipose fin, dorsal fin bud and dorsal fin expression was more similar. Furthermore, we found that some genes relative to the fin development such as tbx5, bmp4 etc, were expressed differently in adipose fin and dorsal fin. These information provided by the comparative transcriptomic analysis may help us to understand the development of adipose fin betterly.