Plasmodium parasites, the causative agents of malaria, undergo a crucial development within the mosquito vector, initiated by the formation of male and female gametes from gametocytes. Male gametogenesis involves three rapid rounds of endomitosis followed by a single round of DNA segregation and nuclear division during gamete budding. How the cell organises the segregation of eight genomes from a single octoploid nucleus is currently unknown. Here, we discovered an atypical five-subunit Arp2/3 complex in Plasmodium essential for DNA segregation during male gametogenesis. Unlike the canonical seven-subunit Arp2/3 complex found in other eukaryotes, Plasmodium Arp2/3 localizes to endomitotic spindles and interacts with the kinetochores. Disruption of key Arp2/3 subunits or actin polymerization impedes proper DNA segregation, resulting in the formation of sub-haploid gametes and halting transmission. Our work identified an evolutionary divergent Arp2/3 protein complex in malaria parasites that offers novel insights into its function and potential targets for transmission-blocking interventions.