AbstractAnt queens can maintain a large number of sperm cells for over a decade after mating at the beginning of their adult lives until they die. This sperm storage ability is prominent; however, the cellular mechanisms involved remain unclear. Sperm cells are maintained in the female sperm storage organ—the spermatheca—which supplies a suitable environment for sperm cells. To reveal the molecular basis of the long‐term sperm storage mechanisms in ant queens, protein profiles enriched in the spermathecal fluid relative to the hemolymph were identified in Lasius japonicus using data‐independent acquisition‐based quantitative proteomics technology. Proteins related to the extracellular matrix, antioxidants, metabolic pathways, proteases, chaperones, and with uncharacterized functions were especially abundant with higher log ratio values in the spermathecal fluid relative to the hemolymph. These enriched proteins were shared with highly expressed genes previously detected by transcriptome analyses of the spermatheca in queens of Crematogaster osakensis that belong to a different subfamily than L. japonicus. It is likely that the ability for long‐term sperm storage evolved early in the ant lineage. Therefore, the common proteins identified in these two ant species are possibly crucial for this ability.