The influence of season and water temperature on the occurence of Harpella melusinae in black fly (Diptera: Simuliidae) larvae was investigated in three streams in northern Thailand. A total of 1260 black fly larvae were examined and 86.3 (CI = 82-88) were colonized by H. melusinae. Both prevalence and level of colonization by H. melusinae varied depending on season (P < 0.01). The highest prevalence was during the cool season (November, 96-100), compared to the wet season (July to October, 80-92) and dry season (April to June, 72-89). The levels of colonization (or numbers of thalli per midgut) by H. melusinae also showed a similar pattern. Regression analysis was significant for season and prevalence at all sites, whereas the level of colonization varied across sites. Prevalence and level of colonization varied with water temperature (P < 0.05), and both were higher in colder waters. This study helps to redress the paucity of ecological information concerning this group of fungi but further studies with different taxa, hosts and habitats will undoubtedly increase our limited knowledge about the ecology of this group of obligately endosymbiontic microorganisms.