The rootlet systems, kinetosomes, and transition zones in zoospores ofPhytophthora parasitica,Thraustochytrium aureum, andRhizidiomyces apophysatusand secondary zoospores ofSaprolegnia diclinaare compared. Rootlet systems inP.parasiticaandS.diclinaare very similar and there are only minor differences between these taxa in morphology of their transition zones. InP.parasiticaandT.aureuma number of differences exist in the rootlet systems, but the position and orientation of individual rootlets are similar. There are also differences between these taxa in the alignment of their kinetosomes, the morphology of their kinetosome cores, and transition zones.Rhizidiomyces apophysatushas rootlets that correspond in position and orientation toP.parasitica, but there are not as many rootlets and these are morphologically distinctive. However,R.apophysatusandS.diclinahave flagellar transition zones that are morphologically alike. Thus, probably the Hyphochytriomycetes are phylogenetically quite closely related to the Saprolegniales and more distantly related to the Peronosporales. In contrast, the Thraustochytriales are distantly related to the Oomycetes and Hyphochytriomycetes, but nonetheless similarities in the flagellar apparatus indicate that all have a common ancestor.