Amplified fragment length polymorphism (AFLP) is a well-established method for DNA fingerprinting. In the last years, fragment separation gradually changed from using gel to capillary electrophoresis, resulting in large, digital data sets. Automatic scoring softwares available to date are proprietary and expensive. tinyFLP/tinyCAT is a compact, open-source software for automatic scoring of AFLP data. It reads from PeakScanner© generated tables, optimizes the conversion of peak data into a binary allelic matrix and removes operator-mediated ambiguities from the scoring process. The output is formatted for direct use in MrBayes and other phylogenetic applications.