We have applied a combination of direct, long-read minion nanopore sequencing of intact mRNA and high-coverage Illumina sequencing of cDNA to survey alternative splicing in Plasmodium and Toxoplasma parasites. These RNAseq experiments reveal considerable alternative splicing in full length transcripts, and major differences in splicing between life stages. The Serine/Arginine-rich (SR) family are the major regulators of alternative splicing, and we have identified multiple SR family in each apicomplexan group studied. We have now modulated parasite SR proteins through knockout, knockdown and overexpression in Plasmodium berghei and Toxoplasma gondii. Disruption of some SR proteins leads to defects in asexual proliferative stages, while disruption of other family members leads to blocks in differentiation between life stages. RNAseq analysis of Toxoplasma and Plasmodium SR mutant parasites reveals major transcriptome-wide changes in alternative splicing. Our data reveal alternative splicing as a highly regulated element of apicomplexan gene expression that is central to proliferation and differentiating. We consider this regulation to be analogous to the changes in alternative splicing required for tissue differentiation and identity in multicellular animals.