The biological importance of rhizosphere sediment-associated fungi in mangroves is poorly understood, especially when they are affected by high salinity and anaerobiosis in disturbed areas. This study evaluated the fungal diversity in the rhizosphere sediments of three mangrove species associated with three conservation conditions of mangrove forests in preserved, semi-preserved, and deteriorated areas. In addition, fungal bioactivity was correlated to the fungal diversity found in mangrove species from each area. We isolated 50 fungal strains belonging to three phyla, seven classes, and 10 orders. The fungal diversity was higher in the preserved area (H' = 2.22) than in the semi-preserved (H' = 1.73) and deteriorated areas (H' = 1.68); the redundancy analysis showed a tendency of fungal accumulation towards the rhizosphere of Rhizophora mangle and Avicennia germinans in the preserved and semi-preserved areas. In addition, the redundancy analysis showed that 10 bioactive fungi genera tended to accumulate on the rhizosphere of R. mangle and A. germinans in the preserved and semi-preserved areas. The preserved area is related to the semi-preserved area, with a 28% Jaccard similarity coefficient. The diversity and bioactivity of the isolated fungi encourage the need to conserve and restore mangrove ecosystems considering their current and potential services, such as bioprospecting new pharmacological compounds.