Abstract Background Mouse models of dysferlinopathies are valuable tools with which to investigate the pathomechanisms underlying these diseases and to test novel therapeutic strategies. One such mouse model is the Dysf tm1Kcam strain, which was generated using a targeting vector to replace a 12-kb region of the dysferlin gene and which features a progressive muscular dystrophy. A prerequisite for successful animal studies using genetic mouse models is an accurate genotyping protocol. Unfortunately, the lack of robustness of currently available genotyping protocols for the Dysf tm1Kcam mouse has prevented efficient colony management. Initial attempts to improve the genotyping protocol based on the published genomic structure failed. These difficulties led us to analyze the targeted locus of the dysferlin gene of the Dysf tm1Kcam mouse in greater detail. Methods In this study we resequenced and analyzed the targeted locus of the Dysf tm1Kcam mouse and developed a novel PCR protocol for genotyping. Results We found that instead of a deletion, the dysferlin locus in the Dysf tm1Kcam mouse carries a targeted insertion. This genetic characterization enabled us to establish a reliable method for genotyping of the Dysf tm1Kcam mouse, and thus has made efficient colony management possible. Conclusion Our work will make the Dysf tm1Kcam mouse model more attractive for animal studies of dysferlinopathies.