Expressed sequence tags (ESTs) are a rich source of SSR sequences, but the proportion of long Class I microsatellites with many repeats vs. short Class II microsatellites with few repeats is an important factor to consider. Class I microsatellites, with more than 20 bp of repeats, tend to make better markers with higher polymorphism. The goal of this study was to determine the frequency of Class I and Class II microsatellites in a collection of over 21 000 ESTs from a single study of five different tissues of common bean: two types of leaves, nodules, pods and roots. For this objective, we used three different bioinformatics pipelines: Automated Microsatellite Marker Development (AMMD), Batchprimer3 and SSRLocator. In addition, we determined the frequency of single or multiple SSRs in the assembled ESTs, the frequency of perfect and compound repeats and whether Class I microsatellites were mainly di-nucleotide or tri-nucleotide motifs with each of the search engines. Primers were designed for a total of 175 microsatellites concentrating on class I microsatellites identified with SSR locator. A few other microsatellites were included from the other search engines, AMMD and Batchprimer3 programs so as to have a representative set of class II markers for comparison sake. The comparison of 95 class I vs. 80 class II markers confirmed that the Class I were more polymorphic and therefore more useful.