Selain Masjid Gedhe Kauman Yogyakarta, di wilayah DIY terdapat lima Masjid Pathok Negoro masing-masing adalah: Masjid Sultan Agung Babadan Baru Bantul DIY, Masjid Pathok Negara Taqwa Wonokromo Bantul DIY, Masjid Sulthoni Plosokuning Sleman DIY, Masjid Jami’ an-Nur Mlangi Sleman DIY, dan Masjid Nurul Huda Dongkelan DIY.