The Halictidae, where the Seladonia aeraria belongs, was an important model organism for studying the evolution of insect social behavior. We first sequenced the complete mitochondrial genome (mitogenome) of Seladonia aeraria. The mitogenome was 15, 410 bp in length, including 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a hypothetical control region. In order to reveal the phylogenetic position of Seladonia aeraria form mitogenomic level, we performed phylogenetic analysis of 13 PCGs from 15 species. The results revealed that the genus-level relationship of Halictidae was Seladonia + Lasioglossum and Seladonia aeraria was more closely related to Seladonia tumulorum than Lasioglossum sp. SJW_2017. The complete mitogenome of S. aeraria will provide a basis for further study evolution and phylogenetic analysis of Halictidae.