The Izumi plain, located in the southern part of Japan, serves as a major overwintering site for endangered crane species, including the hooded crane (Grus monacha) and the white-naped crane (Grus vipio). Since the 2012/13 winter season, continuous surveillance of avian influenza viruses (AIVs) in environmental water and wild birds has been conducted in this region. During the 2023/24 winter season, 45 isolates of H5N1 high pathogenicity AIVs (HPAIVs) and 24 isolates of low pathogenicity AIVs (LPAIVs) were obtained at different time points from crane roost water. Additionally, H5N1 HPAIVs were detected in four wild ducks in November 2023 and in eight cranes in December 2023. Phylogenetic analyses revealed that all H5N1 HPAIVs belonged to subclade G2d of clade 2.3.4.4b, with early winter isolates—particularly those from wild ducks and roost water—occupying more ancestral phylogenetic positions. These findings suggest that wild ducks likely introduced HPAIVs into the overwintering site. Genotype analysis based on the genetic constellations of all eight gene segments indicated the co-introduction of multiple HPAIV genotypes into the Izumi plain and suggested bidirectional gene segment exchange between HPAIVs and LPAIVs. Hemagglutination inhibition assays detected no H5 HA-specific antibodies in six overwintering cranes, implying a limited role for cranes in virus dissemination. Collectively, these findings underscore the importance of continued virological surveillance and genetic monitoring of AIVs at major overwintering sites, where close ecological interactions between wild ducks and cranes facilitate cross-species transmission.