Since 2020, clade 2.3.4.4b H5Nx high pathogenicity avian influenza viruses (HPAIVs) have consistently spread across continents, causing outbreaks worldwide. During the 2023–2024 (23/24) and 2024–2025 (24/25) winter seasons, clade 2.3.4.4b H5Nx HPAIVs caused multiple outbreaks on poultry farms and were detected in wild birds in South Korea. In this study, we present the emergence of clade 2.3.4.4b H5N1, H5N6, and H5N3 HPAIVs and examine the genetic characteristics of these viruses isolated from poultry and wild birds during the 23/24 and 24/25 winter seasons. In the 23/24 season, H5N6 and H5N1 HPAIVs caused outbreaks (poultry: 32, wild bird: 19), whereas in the 24/25 season, H5N3 and H5N1 HPAIVs were detected (poultry: 47 and wild bird: 43). Notably, a novel H5N3 HPAIV was isolated from northern pintail and identified as a reassortant virus distinct from the previously reported H5N3 HPAIV. Phylogenetic analysis of the hemagglutinin (HA) gene showed that viruses from both seasons were closely related to HPAIVs isolated in Eurasia. Gene constellation analysis identified two distinct genotypes of H5N1 viruses (23G0-G1) and one genotype of H5N6 virus (23G2) during the 23/24 season, with the latter being the dominant subtype in that period. In the 24/25 season, five distinct genotypes of H5N1 viruses (24G0–G4) were detected, with 24G1 being the major circulating genotype. Our results suggest that H5N6 HPAIVs appear to be circulating in East Asia alongside H5N1 viruses. Furthermore, in the 24/25 season, two genotypes of H5N1 viruses identified in South Korea were also detected in neighboring countries during the same period: 24G0 was detected in both Korea and Japan, while 24G1 was detected in Korea, Japan, and Mongolia. Therefore, a better understanding of the genetic characteristics of HPAIVs is important for inferring virus introduction and implementing effective control measures in the field.