Blastodinium are chloroplast-containing dinoflag-ellates which infect a wide range of copepods. They de-velop inside the gut of their host, where they produce suc-cessive generations of sporocytes that are eventually expelled through the anus of the copepod. Here, we report on cope-pod 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 East-ern Mediterranean infected, with up to 51 % of Corycaei-dae, 33 % of Calanoida, but less than 2 % of Oithonidae and Oncaeidae. Parasites were classified into distinct morpho-types, 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" clus-ter), and the other uniting all B. spinulosum-like morpho-types (the "spinulosum" cluster). Cluster-specific oligonu-cleotidic probes were designed and tested by fluorescence Correspondence to: L. Guillou (laure.guillou@sb-roscoff.fr) in situ hybridization (FISH) in order to assess the distribu-tion of dinospores, the Blastodinium dispersal and infect-ing stage. Probe-positive cells were all small thecate di-noflagellates, with lengths ranging from 7 to 18 µm. Max-imal 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 distribution of dinospores and nauplii argues against infection during the naupliar stage. Dinospores, described as autotrophic in the literature, may escape the severe nutrient limitation of ultra-oligotrophic ecosystems by living inside copepods.