Blastodinium are chloroplast-containing dinoflagellates which infect a wide range of copepods. They develop inside the gut of their host, where they produce successive generations of sporocytes that are eventually expelled through the anus of the copepod. Here, we report on copepod infections in the oligotrophic to ultra-oligotrophic waters of the Mediterranean Sea sampled during the BOUM cruise. Based on a DNA-stain screening of gut contents, 16% of copepods were possibly infected in samples from the Eastern Mediterranean, with up to 51% of Corycaeidae, 33% of Calanoida, but less than 2% of Oithonidae and Oncaeidae. Parasites were classified into distinct morphotypes, with some tentatively assigned to species B. mangini, B. contortum, and B. cf. spinulosum. Based upon the SSU rDNA gene sequence analyses of 15 individuals, the genus Blastodinium was found to be polyphyletic, containing at least three independent clusters. The first cluster grouped all sequences retrieved from parasites of Corycaeidae and Oncaeidae during this study, and included sequences of Blastodinium mangini (the "mangini" cluster). Sequences from cells infecting Calanoida belonged to two different clusters, one including B. contortum (the "contortum" cluster), and the other uniting all B. spinulosum-like morphotypes (the "spinulosum" cluster). Cluster-specific oligonucleotidic probes were designed and tested by FISH in order to assess the distribution of dinospores, the Blastodinium dispersal and infecting stage. Probe-positive cells were all small thecate dinoflagellates, with lengths ranging from 7 to 18 μm. Maximal abundances of Blastodinium dinospores were detected at the Deep Chlorophyll Maximum (DCM) or slightly below. This was in contrast to distributions of autotrophic pico- and nanoplankton, microplanktonic dinoflagellates, and nauplii which showed maximal concentrations above the DCM. The distinct distributions of dinospores and nauplii argues against infection during the naupliar stage. Blastodinium, described as autotrophic in the literature, may escape the severe nutrient limitation of ultra-oligotrophic ecosystems by living inside copepods.