DNA methylation plays important roles in eukaryotic development. However, studies of DNA methylation in Crustacea are very limited. In the present study, we isolated and identified a DNA methyltransferase 2 (Mar-Dnmt2) gene from the prawn Macrobrachium rosenbergii. The cDNA of Mar-Dnmt2 contained an 1,191-bp open reading frame that encoded a putative Dnmt2 protein of 396 amino acids with the ten motifs characteristic of DNA methyltransferases and exhibiting high identities with other known Dnmt2 homologs (30%–42%). By real-time PCR, an especially high level of Mar-Dnmt2 mRNA was found in the ovary, approximately 5–16 times higher than in other tissues. Moreover, Mar-Dnmt2 mRNA obviously decreased during embryonic development. On the other hand, DNA methylation was detected in this study; about 0.05% of cytosine residues were found to be methylated in the DNA of M. rosenbergii.