The labyrinthulids, aplanochytrids, and thraustochytrids comprise a small group of marine saprobes. These organisms cause little economic or environmental impact, but probably play an important role in nutrient cycling and detritus breakdown in marine habitats worldwide. There have been sporadic incidences of labyrinthulid, aplanochytrid, or thraustochytrid species that have become pathogenic and have had major subsequent economic and environmental effects. One is Labyrinthula zosterae, the causative agent of wasting disease of the eelgrass Zostera marina. This species caused massive decimation of eelgrass populations in the 1930s along the Atlantic coasts of North America and Europe. The dieoff of eelgrass lead to the extinction of the limpet Lottia alveus, which relied on eelgrass as its habitat. This remains one of only two documented extinctions of a species due to disease. Economic impact has been reported as a result of Aplanochytrium haliotidis infestation of abalone mari-culture facilities. These diseases are particularly worrisome because they appear sporadically and with little or no warning. In the interim, the causative organisms probably exist with little harm to the host and only become epidemic when environmental conditions are favorable. Fortunately, at least one isolate of a thraustochytrid also provides a human benefit. Schizochytrium aggregatum is being successfully grown in batch conditions for isolation of ?-3-fatty acids (especially DHA or docohexanoic acid) that the organism produces in abundance. We have undertaken this research to provide an understanding of the phylogeny and taxonomy of these organisms and to increase our basic knowledge about these enigmatic protists. By doing so, we hope to provide a model of evolution that can be referenced by future researchers who may be mining for new dietary supplements or controlling disease. This work includes four main parts: (1) In the first part of this study, we evaluate the phylogenetic position of these organisms within the Eukaryota. (2) Part two examines the phylogenetic positions of taxa within the group in relation to each other. (3) The third part of this work addresses the taxonomic validity of the aplanochytrids. (4) The final section evaluates species concepts within the aplanochytrids.