Haemosporidians are one of the most common parasites infecting birds and often negatively affect host fitness. However, how anthropogenic habitat fragmentation may impact the diversity and infection risk of avian parasites remains less described, especially in habitats induced by the construction of hydroelectric dams. Here, we sampled birds on islands and mainland areas of the Thousand Island Lake (TIL) to describe the prevalence and diversity of avian haemosporidian parasites in fragmented habitats. We used molecular-based methods to detect parasites (Plasmodium, Haemoproteus and Leucocytozoon) and to identify the sex of each bird individual. We compared avian haemospordians between islands and mainland areas to investigate the effects of insularity on parasite diversity and disease risk while accounting for bird phylogenetic relationships, morphology traits and functional traits. Overall, we screened 1100 individuals which belongs to 86 bird species. The prevalence was highest for Leucocytozoon (18.55%), followed by Haemophroteus (14%) and Plasmodium (9.55%). We identified 158 lineages of avian haemospordians in the TIL region, with 95 of them (60%) were new records. We found recued prevalence on islands than on the mainland for overall infections, but this pattern persisted only for Haemophroteus when separated by different parasite genus. In addition, the prevalence of each genus was associated with different avian functional traits including dispersal ability, flocking tendency and migration status, while individual morphology traits play a minor role. Although we found a slight trend of reduced alpha diversity of avian hameospordians on islands, it was insignificant for either the three genera overall or separately. Collectively, our study reveals that habitat fragmentation can partially influence the parasite pressure for island birds, but it may further depend on the specific genus of parasites and the functional traits of birds.