Colletotrichum lindemuthianum, the causal agent of anthracnose in common bean (Phaseolus vulgaris), is one of the most yield-limiting factors worldwide. Anthracnose affects the quality of pods by inducing black, sunken cankers and can also affect petioles, leaf veins and stems where it induces the typical anthracnose sunken lesions. A few years ago, a duplex PCR method that combines amplification of an ITS rDNA segment (CY1/CY2) together with an uncharacterized RAPD-derived amplicon (CD1/CD2) was developed for specific detection of C. lindemuthianum. This study shows that the CD1/CD2 marker corresponds to a portion of an iron permease (Ftr1) pseudogene in the vicinity of the gene encoding for a polyhydroxyproline-rich protein in Colletotrichum. Discrimination with Colletotrichum orbiculare is due to a 15 nt deletion in the CY1 annealing region. The potential of using this genomic region for phylogenetic analysis of the C. orbiculare species complex and detection of their related species is discussed.