Abstract: An extremely efficient method and system for identifying an unknown DNA sample based on probabilistic data structures and machine learning techniques. The method and system can quickly and accurately determine a sample's most likely species, sub-species, or strain. The method and system can identify unknown DNA samples with high accuracy and efficiency (reduced time and resources) without requiring alignment. As such, the method and system is suited to develop innovative applications for, but not limited thereto, many clinical, agricultural, environmental and military/forensic scenarios where the rapid classification of DNA may be of critical utility.