Condensin is a multi-subunit protein complex that regulates chromosome organization, segregation and condensation during cell division in eukaryotes. In Plasmodium spp., the causative agent of malaria, cell division is atypical and the role of condensin is unclear. Here we examine the role of SMC2 and SMC4, the core subunits of condensin during endomitosis in schizogony and endoreduplication in male gametogenesis. SMC2 and SMC4 localize at discrete foci during schizogony, and with a diffuse nuclear distribution during male gametogenesis. ChIP-seq analyses suggest a centromeric location of SMC2/SMC4 only during schizogony. Co-immunoprecipitation data reveal the presence of both condensin complex I and II during male gametogenesis, but only the SMC2/SMC4 heterodimer during schizogony. Finally, knockdown of smc2 and smc4 gene expression revealed their essential roles in parasite proliferation and transmission. This study shows that condensin core subunits (SMC2/SMC4) have differential complex and distinct functions at different stages of the parasite life cycle. RT, AAH and KGLR conceived and designed all experiments. RT, RP, SA, MB, RJW, MZ, ER, AF, DB, ED and SW performed the GFP tagging and conditional knockdown experiments; RRS performed liver stage imaging; RP, MZ, ED and RT performed protein pulldown experiments; ARB performed the mass spectroscopy; RP and DG performed the phylogenetic analysis and molecular dynamics; SA, RP XML, GB, TH, KGLR and RT performed the RNAseq and ChIP-Seq experiments; RP, SA, AAH, KGLR and RT analyzed the data; RP, SA, AAH, KGLR and RT wrote the manuscript and all others contributed to it.