Abstract: Gibel carp (Carassius gibelio Bloch) has been widely used for basic and applied studies on developmental genetics and genetic engineering because of the polyploid background and multiple reproduction modes. In this study, we isolated a positive BAC clone with the fragment (F782-BAC) from a BAC library of F strain based on a 782 bp fragment (F782) specific to F strain revealed by comparative genome surveys between F and A⁺ strains. Shotgun sequencing revealed the complete sequence of the F782-BAC that is composed of 172625 bp containing a complete Tc1-like transposon and six incomplete transposons such as transposase-like transposon, PIF/Harbinger transposon, target-primed reversed transcription (TPRT) transposon, and transpon X-elementtransposon. Using the DIG-labeled F782-BAC sequence as a probe, three positive green fluorescence signals were clearly detected on short arms of three homologous acrocentric chromosomes in mitotic metaphases of both F and A⁺ strains. Moreover, differential screening and sequence analysis of the homologus F782-BAC sequence were performed on the A⁺ strain, and a deleted fragment of 3395 bp was identified in the corresponding F782-BAC sequence of A⁺ strain, in which includes the F strain-specific fragment F782. Furthermore, we developed valuable SCAR markers for discriminating strain F from strain A⁺ in gibel carp. Therefore, the current data provide genetic evidence for polyploidy origin in gibel carp and the identified SCAR markers for the marker-assisted selective breeding in gibel carp.