The aphelids, intracellular parasitoids of algae, have a life cycle similar to zoosporic fungi Chytridiomycota and Blastocladiomycota, and are positioned as a sister clade to all fungi on the recent multigene phylogenetic tree. The fungi and aphelids might possibly have a common ancestor with a complex life cycle somewhat similar to modern zoosporic fungi. To investigate this possibility we have analyzed the genes that increase expression during zoosporogenesis of the blastoclad fungus Blastocladiella emersonii based on the transcriptomic data of Vieira and Gomes (2013), and described the course of sporogenesis at the molecular level. Homologs of genes from the B. emersonii gene set were found in various lineages of the Opisthokonta group, and specifically in the transcriptome of Paraphelidium tribonematis. We calculated the percentage ratios of genes that formed common functional groups and the genes with homologs in various clades of related organisms. We found that zoospore production of a blastoclad fungus is a multi-phase process, where switching of the regulatory elements takes place. The analyzed genes are distributed as follows: 81% are common for all Opisthokonta, 16% are specific for Fungi and only 3% are common to Fungi and aphelids but none are found in the Holozoa lineage. Based on these data we propose a hypothesis on the independent origin of the life cycle in Fungi and Aphelida from a polymorphic ancestor.