In common bean the expressed sequence tags (ESTs) are an important source of gene-based markers such as those based on insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). In this study a total of 200 markers were developed based in genes. The primers were designed flaking the intron regions, comparing the common bean ESTs with the soybean genome. These markers were evaluated for parental polymorphisms using the SSCP (single strand conformational polymorphism) technique and Sequenom MassARRAY system and 53 new marker loci were placed on an integrated molecular map in the DOR364 × G19833 recombinant inbred line (RIL) population. This new linkage map was used to build a consensus map, merging the linkage maps of the BAT93×JALO EEP558 and DOR364×BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041 cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 88 Andean and 5 Mesoamerican genotypes was evaluated with 173 SNP markers using the MassARRAY-platform from Sequenom and the KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. The agglomerative dataset was examined, in order to discover marker-trait associations, using a mixed linear model (MLM) that accounted for population structure and kinship. Some significant associations with drought tolerance were identified, and were consistent with previous findings. In short, this study emphasizes the power of gene-based markers for linkage and association mapping in common bean.