Asexual lineages have been suffered from selective disadvantages due to the lack of beneficial mutations, yet they are still geographically widely distributed, which makes the origin of obligate asexuality become one of the most concerned topic in evolution. Despite many theoretical studies, yet little is known about the genetic basis and underlying mechanisms of asexuality. Here in this study, we address this issue by comparing the genome-wide expression profile of three sexual and three asexual D. pulex lineages.