Evaluation of 450 surface sterilized tissue segments of a seasonal wild legume, Sesbania bispinosa(Jacq.), of coastal sand dunes and mangroves of southwest India yielded 546 isolates comprising 39 endophytic fungi with six dominant taxa(Aspergillus flavus, Aspergillus niger, Cladosporium tenuissimum, Fusarium moniliforme,Penicillium chrysogenum and morpho sp. 1). A consortium of saprophytic, pathogenic and toxigenic fungi exists as endophytes in S. bispinosa. Number of segments colonized,number of isolates obtained, species richness and diversity were higher in S. bispinosa in mangroves compared to coastal sand dunes. Seeds yielded more fungal isolates, but species richness and diversity were low. In spite of low fungal colonization in root segments, the diversity was high. Up to 30–40 % endophytic fungi of S. bispinosa differed between coastal sand dunes and mangroves revealing partial host- and habitat-specificity. As S. bispinosa is extensively used as green manure and forage in southwest India, further studies especially on the bioactive compounds of its endophytic fungi might broaden its range of uses. In addition to conventional morphological techniques, molecular tools would provide precise insight on the endophytic fungi of coastal sand dunes and mangroves. Evaluation of 450 surface sterilized tissue segments of a seasonal wild legume, Sesbania bispinosa (Jacq.), Of coastal sand dunes and mangroves of southwest India yielded 546 isolates comprising 39 endophytic fungi with six dominant taxa (Aspergillus flavus, Aspergillus niger, Cladosporium tenuissimum, Fusarium moniliforme, Penicillium chrysogenum and morpho sp. 1). A consortium of saprophytic, pathogenic and toxigenic fungi exists as endophytes in S. bispinosa. Number of segments colonized, number of isolates obtained, species richness and diversity were higher in S. bispinosa in Seeds yielded more fungal isolates, but species richness and diversity were low. In spite of low fungal colonization in root segments, the diversity was high. Up to 30-40% endophytic fungi of S. bispinosa differed between coastal sand dunes and mangroves revealing partial host- and habitat-specificity. As S. bispinosa is extensively used as green manure and forage in s outhwest India, further studies especially on the bioactive compounds of its endophytic fungi might broaden its range of uses. In addition to conventional morphological techniques, molecular tools would provide precise insight on the endophytic fungi of coastal sand dunes and mangroves.