Estimating positions of beacons based on spatial relationships among neighboring beacons. Beacon reference data defining positions of beacons is stored from beacon fingerprints observed by devices (e.g., enabled with global positioning system receivers). For a received beacon fingerprint having at least one beacon for which the beacon reference data is missing (e.g., from a device without a GPS receiver), beacons in the received beacon fingerprint for which beacon reference data is available are identified. Based on these identified beacons, the missing beacon reference data is calculated. In some embodiments, a set of spatially diverse beacons is selected from the identified beacons prior to calculating the beacon reference data.