The high variability and somatic stability of DNA fingerprints can be used to identify individuals, which is of great value in plant breeding. DNA fingerprint databases are essential and important tools for plant molecular research because they provide powerful technical and information support for crop breeding, variety quality control, variety right protection, and molecular marker-assisted breeding. Building a DNA fingerprint database involves the production of large amounts of heterogeneous data for which storage, analysis, and retrieval are time and resource consuming. To process the large amounts of data generated by laboratories and conduct quality control, a database management system is urgently needed to track samples and analyze data. We developed the plant international DNA-fingerprinting system (PIDS) using an open source web server and free software that has automatic collection, storage, and efficient management functions based on merging and comparison algorithms to handle massive microsatellite DNA fingerprint data. PIDS also can perform genetic analyses. This system can match a corresponding capillary electrophoresis image on each primer locus as fingerprint data to upload to the server. PIDS provides free customization and extension of back-end functions to meet the requirements of different laboratories. This system can be a significant tool for plant breeders and can be applied in forensic science for human fingerprint identification, as well as in virus and microorganism research.