Colletotrichum coccodes has been recognized as one of the causal agents of pepper fruit anthracnose in Bulgaria. Recently, this species has been recorded in pepper fruits in Macedonia. In Bulgaria, the fungus has also been isolated from roots of premature senescent pepper plants but in Macedonia it has not been isolated yet. The purpose of the investigation was to make comparative morphological, cultural and molecular characterization of C. coccodes isolates obtained from pepper fruits and roots in Bulgaria and Macedonia. Additionally, a technique was applied to differentiate among the C. coccodes isolates obtained from roots and other microsclerotia-producing fungi. On the host tissue, C. coccodes developed acervular conidiomata with cup-shaped fruiting bodies accompanied with dark-pigmented, unbranched, thick-walled sterile hyphae called setae. A slimy mass of hyaline, straight, unicellular, fusiform conidia appeared on nutrient media. In a short time, numerous small dark globose setose microsclerotia emerged in the colony starting from its centre and distributing proportionally throughout agar plates. Two PCR primer sets were used to sequences of the ribosomal internal transcribed spacer (ITS1 and ITS2) regions. Single products of ~450 bp and ~350 bp were amplified by the genus-specific (Cc1F1/Cc2R1) and the species-specific primers (Cc1NF1/Cc2NR1), respectively. Morphological, cultural and molecular characterization of the isolates from roots and fruits showed that root rot and fruit anthracnose of pepper were caused by one and the same causal agent determined as C. coccodes. The isolates from roots showed rapid mycelial growth, gave rise to numerous minute microsclerotia and produced conidia only on SSPA. SSPA supported significantly more mycelium growth and sporulation than all other media tested and could be recommended for production of large quantity of conidia. No pattern of genetic variation associated with the organ or geographic origin of the isolates was determined.