DNA methylation is a key mechanism underlying epigenetic regulation. Fruit fly has been considered as a free DNA methylation organism until recently a few studies demonstrated that genomic methylated DNA is prevalent during the early embryonic development; but the overall methylation level in Drosophila is lower than in vertebrates and plants. The putative genomic DNA methylation systerm in Drosophila contains a methyltransferase termed dDNMT2 and a methyl-binding protein dMBD2/3. dDNMT2 shows significant homology to the mammalian methyltransferases DNMT2 family, and dMBD2/3 encodes a protein with distinct homology to mammalian methyl-binding proteins MBD2 and MBD3. Some studies also indicated that methylation pattern varies among different species of Drosophila. This article summarizes the recent progresses in studies of DNA methylation in Drosophila.