The temple had not had an honorific mountain prefix since the time of its founding by Nichiryu and was presided over by a single chief abbot along with Honko-ji Temple (Amagasaki City), but as successive chief abbots later went on to disseminate their teachings, branch temples were founded around the Kinki region, in the Hokuriku district, on the coast of the Inland Sea and even as far as Tanegashima, and Hommon-ryu became established with Honno-ji Temple at its top.
日隆の開山以来、尼崎市の本興寺(尼崎市)とともに山号はなく両山一貫主制をしいていたが、その後、歴代貫主が地方に布教し、日承の時代には末寺が畿内、北陸地方、瀬戸内海沿岸諸国さらに種子島まで広布し、本能寺を頂点とする本門流教団が成立した。