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Background  Microcell parasites are small intracellular protozoans mostly detected in molluscs and can be associated with mortalities. In 2010 and 2011, strong increases in mortality events were reported in different wild beds of the wedge clam  Donax trunculus  Linnaeus, along the Atlantic coast of France and the presence of potential pathogens, including microcells, was investigated.    Methods  Clams collected in different beds showing mortality were examined by histology. Based on histological observations, confirmatory analyses were carried out, including transmission electron microscopy (TEM) and molecular characterization.    Results  Histological analyses revealed the presence of small protozoans similar to microcell parasites in different tissues of  Donax trunculus , particularly in muscular and connective tissues. TEM examination confirmed the intracellular localization of the protozoans. Moreover, the lack of haplosporosomes and mitochondria suggested that the observed parasites belong to the genus  Mikrocytos  Farley, Wolf & Elston, 1988.  Mikrocytos  genus-specific PCR and in situ hybridization results supported the microscopic observations. Sequence fragments of the  18S  rRNA gene shared 75–83% identity with the different  Mikrocytos  spp. described previously, including  Mikrocytos mackini  Farley, Wolf & Elston, 1988 and  M. boweri  Abbott, Meyer, Lowe, Kim & Johnson, 2014. Phylogenetic analyses confirmed that the microcell parasites observed in  Donax trunculus  in France belong to the genus  Mikrocytos  and suggest the existence of two distinct species.    Conclusions  Based on morphological, ultrastructural, molecular data and host information, the two microcell parasites detected in  Donax trunculus  belong to the genus  Mikrocytos  and are distinct from previously described members of this genus. This is the first report of  Mikrocytos  spp. found in France and infecting the clam  Donax trunculus .  Mikrocytos veneroïdes  n. sp. was detected in different wild beds and  Mikrocytos donaxi  n. sp. was detected only in Audierne Bay.    Electronic supplementary material  The online version of this article (10.1186/s13071-018-2692-0) contains supplementary material, which is available to authorized users.

parasites and vectors

Descriptions of Mikrocytos veneroïdes n. sp. and Mikrocytos donaxi n. sp. (Ascetosporea: Mikrocytida: Mikrocytiidae), detected during important mortality events of the wedge clam Donax trunculus Linnaeus (Veneroida: Donacidae), in France between 2008 and 2011