Nucleospora cyclopteri is an intracellular fungal-related parasite that causes microsporidiosis in Atlantic lumpfish (Cyclopterus lumpus), a commercially important species widely used to control sea lice in salmon farming. The parasite causes important economic losses in lumpfish aquaculture, but there is little information on its prevalence or pathogenesis. We compared the sensitivity and efficiency of traditional screening methods using macroscopic and microscopic techniques, with a nested PCR and a newly developed qPCR assay. We also examined the distribution of the parasite in different tissues and quantified parasite loads in fish with and without macroscopic symptoms. Our results indicate that 93.3% of the farmed lumpfish we sampled were infected with N. cyclopteri, including 46% asymptomatic fish without any clinical signs of infection. Asymptomatic fish had much lower parasite loads, quantified using qPCR. The infection was detectable in all tissues, including blood, consistent with systemic infection. While both nested PCR and qPCR assays were more sensitive than traditional screening methods, only the qPCR assay provides a quantitative assessment of parasite loads, which should prove useful for managing microsporidial outbreaks in lumpfish aquaculture.