Several species of the family Culicidae are important vectors of diseases in humans and other animals. Immature stages are filter-feeders of organic particulate matter and microorganisms. Studies on microbial diversity can contribute to the discovery of new substances that can be used in the pharmaceutical industry for food or for biological control. The aim of this study was to isolate and identify the fungi associated with Culicidae larvae found in different habitats (natural and artificial), such as fruit shells, rock holes, lakes, aquatic plants, palm bracts and ceramic pots, in several municipalities of Brazilian Amazonia, especially in the states of Amazonas and Rondônia. A total of 38 fungal lineages were isolated from larvae of Aedes aegypti (L.), Aedes fluviatilis (Lutz), Trichoprosopon digitatum (Rondani), Anopheles argyritarsis argyritarsis Robineau-Desvoidy, Anopheles darlingi Root, Aedeomyia squamipennis (Lynch Arribálzaga), Mansonia titillans (Walker) and Uranotaenia sp. The following fungi occurred associated with the larvae of Culicidae: Acremonium kiliense, Aspergillus sydowii, Fusarium sacchari var. sacchari, Fusarium merismoides var. merismoides, Gliocladium viride, Paecilomyces sp., Penicillium citrinum, Penicillium sclerotiorum, Penicillium melinii and Penicillium oxalicum. Macro- and microscopic characteristics of the lineages are presented, as well as information on their geographical distribution.