For newly established protected areas, it is important to document the abundance, structure and distribution of the species within the landscape. Here we assessed the variation in total abundance as well as female, male and juvenile abundance of Mwanza flat-headed rock agama (Agama mwanzae) in Saanane National Park, Tanzania, in relation to daylight condition (sunny and non-sunny) and proximity to humans. Twenty-three points of 50-meter radius were randomly placed and thoroughly searched for A. mwanzae. Of 364 individual Mwanza flat-headed rock agamas recorded, 85% were adults and 15% were juveniles. Among adults, 45% were males and 55% were females. Daylight condition was observed to affect total abundance and the abundance of females, males and juveniles of A. mwanzae, with higher abundance being in sunny periods as compared to non-sunny periods. Distance from the tourist trail was the best predictor for total abundance and the abundance of females and juveniles but not males, with abundance decreasing moving away from the tourist trail. Therefore, we suggest these factors be considered when surveying agamas elsewhere.