The fastidious basidiomycete Ceratobasidium theobromae (P.H.B. Talbot & Keane) Samuels & Keane is a biotrophic pathogen that causes vascular-streak dieback (VSD) of Theobroma cacao L. (cocoa). The fungus biology remains enigmatic, though several studies have progressed knowledge on pathology within the host. Basidiospores, released pre-dawn from rainfall-induced sporophores are the assumed inoculum that infect young leaves (Keane and Prior, 1991). The fungus is difficult to culture in vitro due its slow growth, and colonies are overrun by commensal fungi, thereby hampering inoculation studies and Koch’s postulates. C. theobromae has recently been identified as the cause of emergent diseases in southeast Asia and the Americas, including Cassava Witches Broom Disease of Manihot esculenta Crantz (cassava), and of VSD of Cercis canadensis L. (redbud), raising serious concerns that the pathogen is spreading globally. Should the pathogen reach West Africa, the major world producer and supplier of cocoa beans, the dual effect on both staple and economic crops would be devastating. However, there is no evidence that isolates from cocoa are virulent on cassava or other hosts, or whether the species includes host-specific populations. Fungal homeodomain (HD) transcription factor mating-type (Mat) loci are known to be polymorphic within the Basidiomycota. To understand diversity within C. theobromae we have developed an assay based on the HD alleles by sequencing long amplicons on Oxford Nanopore MinION followed by an analysis pipeline. Our preliminary work has shown that this method may be useful to distinguish host and regional variation within the species.