Introduction: Highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b has spread widely across South America, but its genomic diversity and patterns of introduction into Ecuador remain poorly characterized.Methods: In this study, we report and characterize four genomes of A(H5N1) viruses detected in four individuals of two Ecuadorian seabird species: two magnificent frigatebirds (Fregata magnificens) and two blue-footed boobies (Sula nebouxii) sampled in 2023.Results: These genomes represent confirmed detections of avian influenza in wild birds in the country. The viruses were assigned to genotype B3.2. Global phylogenetic analysis showed that the Ecuadorian wild-bird viruses formed groups distinct from viruses detected in domestic birds in Ecuador. Subsequent phylogenetic and phylogeographic analyses within the South American dataset placed our samples in two distinct clusters, each closely related to viruses previously detected in Peru. These findings highlight the genetic diversity of genotype B3.2 viruses detected in Ecuador and their relationship to viruses circulating in the region. FluServer screening identified 29 amino acid substitutions previously associated with virulence, antigenic change, host specificity, polymerase activity, or antiviral resistance.Discussion: These findings provide genomic evidence of repeated H5N1 introductions into Ecuador as part of the regional spread of the virus along the eastern Pacific coast. They also support sustained surveillance across wildlife, animal-health, and public-health sectors.