Two-spotted goby Gobiusculus flavescens from the Swedish Gullmarsfjord regularly present subcutaneous creamy-white patches in the body musculature, associated with Kabatana sp. infection. Analysis of the 16S rRNA gene of the microsporidium showed 98.54% homology with Kabatana newberryi infecting a marine goby from California, indicating that the Swedish microsporidium is either a different strain of K. newberryi or a closely related species. This represents the first record of a Kabatana species in the Atlantic Ocean. The genetic similarity of the 2 microsporidia was paralleled by close infection phenotypes. Infected muscle fibres were swollen compared to adjacent non-infected fibres, and mature spore masses were found throughout the skeletal musculature. No xenoma formation was detected. Since G. flavescens is an established model species in behavioural ecology, the host–parasite system is ideally suited for testing how microsporidian infections affect host behaviour and fitness.