The basic characteristics of Palaeminidae mitogenomes were revealed by the comprehensive mitogenome analysis of 14 Palaeminidae species. The results showed that the lengths of the 14 mitogenomes varied from 15396 bp to 15967 bp. The content of A + T ranged from 58.97% to 69.09%. Compared with the gene order of a Decapoda ancestor, the gene arrangement order of the Macrobrachium had not changed, but the gene arrangement order of Palaemon, Anchistus, and Hymenocera changed to varying degrees. Furthermore, gene deletion was detected in the mitogenome of Anchistus. The Ka/Ks ratios of 13 protein coding genes (PCGs) in Palaemon and Macrobrachium was much lower than one, indicating strong purification. In addition, the codon usage of the 13 PCGs in Palaeminidae showed that the encoded amino acids had similar preferences. Among the two rRNA genes and 13 PCGs identified the mitogenome, the analysis of the different sites between Palaemon and Macrobrachium showed that the genes nd5, nd4, and nd2 were ideal molecular markers. The phylogenetic trees based on the 13 PCGs showed that Palaemon and Macrobrachium were sisters, and Anchistus and Hymenocera were gathered together into a large branch. Finally, according to the estimation results of the molecular clock, it is speculated that Palaeminidae species may have originated in the Permian, before further differentiating into a species with modern characteristics. This study provides a reliable molecular marker for the rapid identification of Palaeminidae species and a theoretical basis for analyzing the genetic diversity of Palaeminidae species.