Methods and systems are provided for prioritizing frequencies in femtocell frequency-hopping pilot beacons. The frequency-hopping pilot beacon may prioritize transmission on particular frequencies according to usage of one or more particular applications by mobile devices served by the femtocell. The femtocell and/or femtocell control elements in the macro-network may determine that one or more particular applications are used by mobile devices served by the femtocell, identify one or more frequencies associated with the one or more frequencies, and then cause the femtocell to prioritize transmission on the identified one or more frequencies as compared to other frequencies.