Several ecological factors have been proposed to describe the mechanisms whereby host ecology and the environment influence the transmission of Avian Influenza Viruses (AIV) in wild birds, including bird's foraging behavior, migratory pattern, seasonal congregation, the rate of recruitment of juvenile birds and abiotic factors. However these ecological factors are derived from studies that have been conducted in temperate or boreal regions of the Northern Hemisphere. These factors cannot be directly translated to tropical regions where differences in host ecology and seasonality may produce different ecological interactions between wild birds and AIV. An extensive dataset of AIV detection in wildfowl and shorebirds sampled across tropical Africa was used to analyze how the distinctive ecological features of Afro-tropical regions may influence the dynamics of AIV transmission in wild birds. The strong seasonality of rainfall and surface area of wetlands allows testing how the seasonality of wildfowl ecology (reproduction phenology and congregation) is related to AIV seasonal dynamics. The diversity of the African wildfowl community provides the opportunity to investigate the respective influence of migratory behavior, foraging behavior and phylogeny on species variation in infection rate. Large aggregation sites of shorebirds in Africa allow testing for the existence of AIV infection hotspots. We found that the processes whereby host ecology influence AIV transmission in wild birds in the Afro-tropical context operate through ecological factors (seasonal drying of wetlands, extended and non-synchronized breeding periods) that are different to the one described in temperate regions, hence resulting in different patterns of AIV infection dynamics.