A protozoan parasite identified by histology as a haplosporidian was detected in carpet shell clam Ruditapes decussatus from Spain during routine samplings. Analysis based on the sequence of the small subunit ribosomal RNA gene revealed that this organism was related to the haplosporidian group, mainly to Urosporidium. A specific probe was used for in situ hybridization studies to show the specificity of the amplified sequence.