Amazonian fungal identification is crucial to unravel their biodiversity and to elucidate their potential use in several industrial and biotechnological processes. This research aims to isolate and identify Aspergillus niger from Ecuadorian Amazon region in order to assess their capability to produce citric acid from sugar cane bagasse fermentation. Sampling point were settled to perform the distribution pattern of the fungi in the main areas of sugar cane production in Puyo municipality. For isolation, raw material was placed under humid chambers to produce sporulation. After growth, isolates were plated in Potato Dextrose Agar media for purification. Morpho-cultural characterization were assessed for isolates identification . A complete randomized experimental design was conducted under controlled conditions to search out the capability of isolates to produce citric acid. Six days fermentation at pH 2 and three levels of substrates loading (20, 30 and 40 mg bagasse L-1) were the experimental variables. Bagasse was cut into small pieces to homogenization and a concentration of 1x107 spores ml-1 was inoculated. Morpho-cultural analysis threw four isolates with features related to A. niger. Black aerial mycelia, fast growth and copious sporulation matched with the main characteristics of the fungus. The citric acid assay showed the most favourable conditions were provided by the substrate loaded with 30 mg L-1 of bagasse, which yielded 9.9 g of citric acid per kilogram of bagasse. These results show the potential of native Amazonian A. niger to produce citric acid and to perform another trials with other raw material under different conditions.