This study provides morphological, ultrastructural and phylogenetic characterization of 2 novel species of the order Haplosporida (Haplosporidium echinogammari n. sp. and H. orchestiae n. sp.) infecting amphipods of the genera Echinogammarus and Orchestia collected in southwestern England. Both parasites infect the connective tissues associated with the digestive gland and the tegument, and eventually infect other organs causing disruption of host tissues with associated motor impairment and fitness reduction. Prevalence of infection varied with host species, provenance and season, being as high as 75% for individuals of E. marinus infected with H. echinogammari in June (n = 50). Although no spores were found in any of the infected amphipods examined (n = 82), the morphology of monokaryotic and dikaryotic unicellular stages of the parasites enabled differentiation between the 2 new species. Phylogenetic analysis of the new species based on the small subunit (SSU) rDNA gene placed H. echinogammari close to H. diporeiae in haplosporidian lineage C, and H. orchestiae in a novel branch within Haplosporidium. An additional 25 new haplosporidian SSU rDNA sequences were generated from crab, isopod, and crayfish samples, significantly increasing the number of crustacean-derived sequences within Haplosporida, which was previously thought to comprise mostly parasites of molluscs. Phylogenetic analysis of these new sequences revealed 3 clades of primarily crustacean-derived sequences within Haplosporida.