The method and apparatus of the present invention provide for automatic recognition of fingerprint images. In an acquisition mode, subsets of the feature points for a given fingerprint image are generated in a deterministic fashion. One or more of the subsets of feature points for the given fingerprint image is selected. For each selected subset, a key is generated that characterizes the fingerprint in the vicinity of the selected subset. A multi-map entry corresponding to the selected subset of feature points is stored and labeled with the corresponding key. In the recognition mode, a query fingerprint image is supplied to the system. The processing of the acquisition mode is repeated in order to generate a plurality of keys associated with a plurality of subsets of feature points of the query fingerprint image. For each key generated in the recognition mode, all entries in the multi-map that are associated with this key are retrieved. For each item retrieved, a hypothesized match between the query fingerprint image and the reference fingerprint image is constructed. Hypothesized matches are accumulated in a vote table. This list of hypotheses and scores stored in the vote table are preferably used to determine whether a match to the query fingerprint image is stored by the system.