Flagella and cilia are conserved eukaryotic organelles whose formation depends on membrane trafficking, but how this is coupled to axonemal architecture and functional diversification remains unclear. RAB23, a small GTPase known for its role in Sonic hedgehog signaling, has an elusive function in ciliogenesis because its loss is embryonic lethal in animals. Here we analyze RAB23 in the liverwort Marchantia polymorpha, where motile flagella are confined to spermatozoids. Loss of MpRAB23 causes severe defects in spermatozoid morphology, motility, and 9 + 2 axonemal organization, while leaving vegetative growth unaffected. During spermiogenesis, MpRAB23 localizes to elongating flagella and is required for flagellar membrane organization, including polarized localization of MpPOFCAP, a calcium pump confined to the posterior flagellum. Disruption of MpPOFCAP reduces spermatozoid motility and fertility without affecting axonemal structure. These findings identify RAB23 as a regulator of flagellar biogenesis and uncover a specific mechanism by which asymmetric membrane protein targeting differentiates structurally similar flagella within a single cell.