Sequence data of the genome provides valuable information and tools for genetics and genomics research. Next generation sequencing offers new insights useful for marker development. This enables us to compare genotypes at the nucleotide level to design accurate and user-friendly molecular tools. Common bean (Phaseolus vulgaris) is a diverse crop in which separate domestication events in each genepool followed by race and market class diversification has resulted in different morphological characteristics in each market class. This has led to separate breeding programs within each market class which in turn have resulted in their limited sequence variability. Sequence data from selected genotypes of four bean market classes (pinto, black, navy and kidney) allowed the development of indel-based markers specific to each market class. Design of these markers was conducted through a combination of appropriate assembly, alignment and primer design software using 2x to 4.5x coverage of Illumina GAII sequence data for each of the selected genotypes. The procedure we developed for primer design is fast, accurate and less error prone with a higher throughput than when they are designed manually and the user-friendly market class specific indel markers are easy to run and score with no need for PCR optimization. They were used for phylogeny and other population diversity analyses which highlight the usefulness of these indel markers.