Molecular markers play a significant role for crop improvement in desirable characteristics, such as resistance to disease, high growth rate and other characteristics that will benefit the plant and variety in long term. Microsatellites, also known as simple sequence repeats (SSRs) or simple tandem repeats (STRs), have extensively been exploited as molecular markers for diverse applications including genome characterization and mapping. Recently, their role in gene regulation and genome evolution has also been discussed widely. We have developed BanSatDb (Banana Microsatellite Database), a web based relational database of microsatellites present in the whole genome marker discovery having 1.1 lakh markers from 11 chromosomes of M. acuminata, 1.07 lakh markers from draft sequence of M. balbisiana and 1.24 lakh markers from recently published M. itinerans draft assembly, along with 580 markers mined from published literature in common platform using MySQL, Apache and PHP in BanSatDB, a Banana Microsatellite Database. The markers can be retrieved through multiple search parameters like chromosome number (or numbers), microsatellite type (simple and compound), repeat type (mono- to hexa-nucleotide), copy number, microsatellite length, pattern of the repeat motif itself and the location of the marker on the chromosome. These markers can be used for DUS test of variety identification and MAS in variety improvement program. They are also proved to be helpful in classification of Musa germplasm to distinguish individual accessions and in the development of a standardized procedure for genotyping. These marker can also be used in gene discovery and QTL mapping. Database presents wide source for developing and implementing new approaches for molecular breeding, which are required to accelerate the crop productivity.