Black dot is a blemish disease of potato caused by the fungus Colletotrichum coccodes (Wallr.) Hughes. C. coccodes has no known sexual cycle, but genetic exchange is possible through vegetative conjugation. Eight VCGs have been identified for the Europe/Israel population, seven for the North American population, and six for the Australian population. Variation in aggressiveness, morphological traits, and physiological traits have been detected among the different C. coccodes VCGs. AFLP markers could separate the five VCGs of C. coccodes isolates, coinciding almost completely with the six VCGs of nit mutants. Additionally, a relationship of specific AFLP bands to corresponding VCGs was reported using AFLP analysis. The objectives of this study were: to develop VCG-specific sequence characterized amplified regions (SCAR) markers, to study the population biology of C. coccodes of North America using AFLP method, and to study genetic diversity of the global populations of C. coccodes . Only one SCAR primer, AGb6F/R, with 156 bp amplification PCR product was found to be specific for NA-VCG6 and NA-VCG7 of C. coccodes. For the second objective, C. coccodes isolates recovered from potato plants were assigned to four NA-VCGs, NA-VCG1, NA-VCG2, NA-VCG4/5, and NA-VCG6/7. No isolates tested belonged to NA-VCG3. NA-VCG2 was the dominant and the most frequent group among states, fields, farms, and plants. However, in several instances there was more than one NA-VCG recovered from the same plant, field, farm, and state, indicating variability within the C. coccodes population in United States. Genetic differentiation among the nine states was 0.331, and overall gene flow for the 366 isolates was (N_m = 1.01). For the genetic diversity of the global C. coccodes population, results showed that the population of C. coccodes exists as one large population with four main groups (NAVCG1/3; NA-VCG2; NA-VCG4/5; and NA-VCG6/7). NA-VCG5 was the most common VCG globally followed by NA-VCG2. Among the five regions studied, there was relatively low gene diversity (0.222). The overall gene flow (Nm) was 1.25, meaning that one or more individuals are exchanged among the five regions each AFLP analysis proved to be valuable in differentiating and studying the global population of C. coccodes .