Common bean (Phaseolus vulgaris) is an agronomically important legume especially in developing countries. Common bean is very diverse, consisting of two major geographically distinct gene pools, Andean and Mesoamerican, each with three or four races. Currently, the genome sequence of Andean domesticated accession G19833 is in progress, thus enabling exploration of common bean at genome level. To provide a useful resource for the study of genome evolution and breeding in common bean, we developed FISH-based karyotype map of common bean using repetitive sequences and BAC clones. Karyotype map is a powerful tool to identify individual chromosomes, understand chromosome behavior and study genome evolution. First, we identified two high copy tandem repeats, CB100 and CB110 based on tandem repeat analysis from common bean draft genome sequence and bacterial artificial chromosome end sequences (BES). Fluorescence in situ hybridization (FISH) using these two repeats on metaphase chromosomes confirmed that they were located at centromeres. A probe cocktail for a karyotype map was developed using these two repeats, CB100, CB110, ribosomal RNA genes, subtelomeric repeats khipu and BAC clones to identify all of the chromosomes simultaneously. With the developed probe cocktail, the karyotype of a wide collection of common bean has been analyzed in terms of repeat distribution and chromosomal structural variation. This data contribute to provide useful information for the study of genome evolution, chromosomal structural variation, and breeding strategy in common bean.