The silkworm Bombyx mori TWPB strain has a large chromosome formed by the fusion of the W chromosome with a fragment of chromosome 2 and chromosome 5. The chromosome 2 region of chromosome W-II-V has p^B mutation which causes the larval integument to be black. Larvae with exceptional phenotypes—such as black (p^B) and moricaud (p^M) males that are presumably generated by fission event occurring in chromosome W-II-V—occasionally occur during the maintenance of the TWPB strain. In the p^M male progenies, segregated in the TWPB strain, fragment consisting of chromosome 2 and 5 dissociate from W-II-V chromosome and fuse with chromosomes Z and 13, generating two new fused chromosomes Z-II-V and XIII-II-V. Using bacterial artificial chromosome clones and fluorescent in situ hybridization (BAC-FISH mapping), we analyzed the structure of the fused chromosomes. We also analyzed their structures using the recombination values between p^M and phenotypic markers in the chromosomes Z and 13. Further, using a PCR-based molecular marker, we confirmed that no protein-coding genes on chromosomes Z and 13 were lost due to the fusion events. Moreover, we found through the crossing experiments with Z-II-V strain that the fusion resulted in the formation of neo-Z/W neo-W sex chromosome constitution. The TWPB strain and the TWPB-derived-novel-fusion-carrying strains are useful for the genetic and molecular cytogenic analysis of the chromosomal rearrangements in lepidopterans.