This study aimed to inventory fungal populations associated with the rhizosphere of Avicennia germinans in different salinity levels in a semi-arid mangrove in the Colombian tropics. Targeting the ITS1 and ITS2 regions provided complementary information, allowing a better approach to inventorying the fungal biodiversity. Amorosia and Aspergillus were the most abundant ascomycete genera, while Cystobasidium was the most abundant basidiomycete genus. Only five genera showed significant differences in abundance among the three salinity levels. Nevertheless, 65.4% of the genera were classified as exclusive for a specific salt content. Saprotrophs were the most abundant functional group and symbiotrophs were detected as mycorrhizas, fungi with biocontrol activity and entomopathogenic activity. These ecological groups play an important role in the cycling of organic matter and the availability of nutrients for mangrove plants and their tolerance to environmental and biotic stresses. This study highlights soil salinity as a determining factor in the composition of the fungal community in mangroves.