Rhopalosiphum nymphaeae (Linnaeus, 1761) is a heteroecious polyphagous aphid, which can survive underwater. We have determined mitochondrial genome of R. nymphaeae collected in Korea. The circular mitogenome of R. nymphaeae is 15,594 bp including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 874 bp. The base composition was AT-biased (84.3\%). Phylogenetic trees present that genus Rhopalosiphum is polyphyletic, requiring more investigation of mitochondrial genomes.