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Lasiodiplodia theobromae is a common pathogen that occurs on a large number of hosts in the tropics and subtropics. A collection of isolates identified as L. theobromae was studied on the basis of sequence data from the ITS regions and EF1-α gene. Phylogenetic analyses identified three well-supported clades within this group of isolates, one corresponding to L. theobromae and two others corresponding to potential cryptic species. The distinct phylogenetic position of the two clades is supported by differences in conidial morphology and these are, therefore, described as Lasiodiplodia pseudotheobromae sp. nov. and Lasiodiplodia parva sp. nov.