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GaN nanowires were grown using selective area plasma-assisted molecular beam epitaxy on SiOx/Si(111) substrates patterned with microsphere lithography. For the first time, the temperature–Ga/N2 flux ratio map was established for selective area epitaxy of GaN nanowires. It is shown that the growth selectivity for GaN nanowires without any parasitic growth on a silica mask can be obtained in a relatively narrow range of substrate temperatures and Ga/N2 flux ratios. A model was developed that explains the selective growth range, which appeared to be highly sensitive to the growth temperature and Ga flux, as well as to the radius and pitch of the patterned pinholes. High crystal quality in the GaN nanowires was confirmed through low-temperature photoluminescence measurements.