Identifying the dominant slip systems in naturally deformed quartz is crucial for understanding continental crust rheology. Although the basal <a> slip system is considered dominant in quartz under upper to middle crustal conditions, its activity is controversial because an oriented nucleation and growth model has been proposed for the c-axis distribution near the minimum strain axis. This study examined the crystallographic orientation and shape of quartz phenocrysts in a deformed granitic porphyry in the Ryoke belt, SW Japan, to clarify the dominant slip systems in naturally deformed quartz at temperature conditions of ∼400–500 °C utilizing optical and electron backscatter diffraction (EBSD) observations. Identified active slip systems include prism <a>, basal <a>, prism [c], and rhomb <a> through misorientation analyses. The aspect ratios of phenocrysts with dominant prism <a> and basal <a> slip systems are higher than prism [c] and rhomb <a> slip systems, indicating similar strengths between prism <a> and basal <a> slip systems, which are weaker than prism [c] and rhomb <a> slip systems under lower amphibolite-facies conditions. The c-axis of phenocrysts with dominant basal <a> distribute at pole figures peripheries, indicating basal <a> activation over the proposed oriented nucleation and growth model.