A potentially fatal microsporidial infection targeting the skeletal muscles of the tiger barb Puntius tetrazona was described. Ultrastructural and molecular analyses of infected tissues confirmed that the causative parasite was Pleistophora hyphessobryconis. Compared to P. hyphessobryconis observed in other hosts, those infecting tiger barb demonstrated differences in ultrastructure that may be related to host adaptation. Phylogenetic analysis revealed that classifications based on different methods of analysis (molecular, morphologic, or developmental) do not always coincide, and suggesting that the genetic relationships between Pleistophora and Ovipleistophora may need to be redefined. Transparent mutants of tiger barb can be artificially infected by P. hyphessobryconis, and the dynamic process and spatial distribution of P. hyphessobryconis infection can be observed in real time. These transparent fish mutants are a valuable model to study microsporidial infection in vivo.