Mangroves forests are located in tropical and subtropical regions, its adaptation and distribution in coastal regions is influenced by temperature, humidity, tidal and saline fluctuations. Therefore, there are exposed to multiple environmental fluctuations. Mangroves are inhabited by wildlife but also is supported by a diverse community of microorganisms, including fungi. Several fungi in mangroves have multiple ecological roles as saprotrophs or as an opportunistic pathogen, many of them are also used in the industry, as the genus Aspergillus, that are important in the biomedicine, industrial and environmental applications. In this study we isolated species of fungi from mangrove stems and propagules. They were identified by both morphological and by its molecular characteristics. Here, we report the first isolated of Aspergillus niger and Aspergillus aculeatus from mangrove in Ecuador. Research such as these highlights the importance to determine the role of fungi in mangrove ecosystem.