Osmotrophic eukaryotes with a cell wall during the assimilative phase are ‘fungi’: the term ‘fungus’ is an essentially physiological concept, thus flagellate fungi conforming to this definition are not ‘pseudofungi’. But mycologists may also work with flagellate organisms which are phagotrophic or lack a plasmodial cell wall and, therefore, are not strictly ‘fungi’. In fungi the flagellate stage is confined to planonts (asexual zoospores and gametes).

Flagellar form and function have many conserved characteristics, but although ultrastructural diversity, particularly in kinetosome/flagellar root structure, has been intensively studied, other morphological features of the zoospore have been less thoroughly explored. The numbers, lengths, orientations and structural ornaments of flagella all provide data for biodiversity assessments at the species and ecological levels. The structural and functional biodiversity of fungal flagella and zoospores are reviewed, particularly with respect to the isokont/anisokont flagellar lengths and the isokont/heterokont flagellar ornaments of the zoospore. The straminipilous ornamentation has particular functional significance.

Correlations between molecular biology and flagellar ultrastructure indicate that several independent phylogenetic lines have evolved flagellate fungi. The strengths and weaknesses of the databases for these phylogenies are discussed in historical and current contexts.