Anthracnose, caused by the fungus Colletotrichum lindemuthianum , is considered a major constraint in the production of common bean ( Phaseolus vulgaris L.). This study aimed to evaluate, in a backcross plant‐breeding program, the efficiency of selecting plants resistant to anthracnose using marker‐assisted selection (MAS) for two resistance genes, Co‐5 and Co‐4 2 derived from the resistance source G2333 based on the linked PCR based markers SAB3 and SAS13. The amplification of both markers was compared using DNAs extracted with two techniques, alkaline extraction, which is a fast, and inexpensive method for high throughput screening; versus a proteinase K based miniprep extraction, which is more time consuming but provides more DNA. To further evaluate the effectiveness of the markers in selecting for resistance, we compared the marker genotypes and observed phenotypes for 266 plants from eight backcross families inoculated with a field isolate of anthracnose. The Co‐5 gene and SAB3 proved to be useful and the markers associated with Co‐5 and Co‐4 2 could be pyramided to give added levels of anthracnose resistance.