Black root rot (BRR), incited by the soil born pathogen Thielaviopsis basicola is an interesting host-pathogen system to study evolutionary differences leading to R-gene formation and divergence in cotton (Gossypium spp). Tetralopid cotton (G. hirsutum and G. barbadense) are highly susceptible; however, resistant types have been identified in A-genome diploid cotton (G. herbaceum var. “A20”).  Genetic mapping was used to determine the chromosomal locations of quantitative trait loci (QTLs) that confer resistance to the BRR pathogen.  A population of F2 individuals (G. herbaceum X G. arboreum) and F3 progeny families was examined using 159 simple sequence repeats (SSR). A genetic component that controls resistant and susceptible reactions resulting from T. basicola infestations could be explained by two QTLs. The QTLs on Chromosomes 1 (Rtbq1) and 10 (Rtbq10) each explained 15.1 and 11.9% of the total phenotypic variation, respectively.  A focus to determine the underlining DNA sequence of these R-genes is a key step toward studying their evolution in Gossypium. Research activities to clone each gene and transfer resistance into Upland cotton are ongoing.