The silkworm Bombyx mori carries a holokinetic (holocentric) chromosome and has a female heterogametic sex determination system (WZ/ZZ chromosomes, female/male). Homologous chromosomes form directional synaptonemal complexes during primary meiosis. The WZ sex chromosomes have a bivalent form; however, the direction of their pairing has long been unknown. In this study, our fluorescence in situ hybridization-based analysis revealed that the W and Z chromosomes form a non-directional bivalent during primary meiosis.