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The kingdom Straminipila (Stramenopiles) is defined by the possession of an ornamented “straminipilous” or “tinsel” flagellum. With flagella being central to the classification of these organisms, it stands to reason that the genes controlling flagellar structure and motility should be able to provide some interesting insight into the evolution of different species and genera of oomycetes. Ultrastructural studies have already revealed the connection between flagellar apparatus morphology and phylogeny of zoosporic fungi. This concept has now been explored at the molecular level, with DNA sequencing of an axoneme central apparatus gene (ACA) and a tinsel flagellum mastigoneme gene (OCM1) from a variety of Peronosporales (eg. <i>Pythium</i>, <i>Phytophthora</i>) and Saprolegniales (eg. <i>Saprolegnia</i>, <i>Aphanomyces</i>) species using degenerate primers. The phylogenetic reconstructions obtained from ACA and OCM1 are well supported and in accordance with current views of oomycete systematics. Interestingly, the OCM1 amino acid sequence is highly variable between species, but highly conserved within species. Such a species-specific nature suggests that OCM1 may play an important ecological role, possibly in oomycete interaction with hosts, and could be used to better define species boundaries in oomycetes.<p><p>Keywords: Oomycete