Hox genes are important regulatory factors of transcription in metazoans, and are involved in the growth and development of organisms. In this study, the effects of Microcystis aeruginosa on Hox gene expression in the mothers and offspring of Daphnia similoides sinensis were investigated using a mixed diet of M. aeruginosa and Scenedesmus obliquus in two clones. The 14 Hox genes sequence were identified in D. similoides sinensisare through the previous transcriptome data (Zhang et al., 2016. DOI: 10.1038/srep34241).