Fusarium isolates obtained as endophytes from healthy leaves of Handroanthus chrysotrichus (Bignoniaceae) in the Atlantic Forest of north-eastern Brazil were characterised morphologically and phylogenetically on the basis of partial rDNA sequences encompassing the second largest subunit of RNA polymerase II, translation elongation factor EF-1 alpha, and β-tubulin genes. A novel species within the Fusarium lateritium species complex (FLSC) is described as Fusarium massalimae. Isolates of F. pseudocircinatum of the Fusarium fujikuroi species complex (FFSC) were also isolated as endophytes from leaves of H. chrysotrichus. Mating type gene analyses suggested that obtained isolates of F. massalimae and F. pseudocircinatum are heterothallic.