Ramulosis of cotton, caused by Colletotrichum gossypii var. cephalosporioides (CGC), is an important disease of cotton in Brazil. The main objective of this work was to test whether CGC is a phylogenetic species inside the Colletotrichum gloeosporioides species complex. A Bayesian inference phylogenetic analysis of a combined ITS and TUB2 dataset was conducted with 21 strains identified as CGC and five strains of Colletotrichum gossypii (CG), associated with cotton anthracnose, obtained from diseased plants from different regions of Brazil. All CGC strains formed a highly supported lineage inside the clade of Colletotrichum theobromicola, a member of the C. gloeosporioides species complex. CG strains formed another lineage in the same clade. These findings were supported by a second analysis conducted with three genes (ITS+TUB2+GAPDH) and a subset of five CGC and three CG strains. During pathogenicity tests, all five CGC strains tested induced typical symptoms of ramulosis on inoculated plants, including foliar necrosis, death of apical meristems and over sprouting. Plants inoculated with CG strains exhibited foliar necrotic spots two months after inoculation. These results give phylogenetic support for the placement of CGC in the C. gloeosporioides species complex, and the distinction between the ramulosis and anthracnose pathogens of cotton in Brazil.