Verrucaria nigrescence Pers. has a high tendency to grow on calcareous rocks but it rarely found on rich rocks in silica of Khorasan Razavi province located in the Northeastern zone of Iran. Based on extensive studies, the relationship between favorite substrate and distribution of lichens is clear; but, there are few studies regarding the effects of suboptimal substrate and insect’s behavior on morphological and anatomical characteristics. Therefore, 35 thalli of V. nigrescence were collected from both calcareous and siliceous rocks in the mentioned region. 33 quantitative and 19 qualitative morphological and anatomical characters were analyzed by independent t-test and Pearson chi-square test. Results showed that siliceous samples had a higher algal layer and excipulum and involucrellum width in the specimens growing on suboptimal substrates were smaller than normally developed species. A significant medulla observed below the perithecia of some siliceous samples that attracted insect’s colonies. Our investigation agreed with earlier studies using the other species which shown unfavorable substrate had a prominent effect on some features; but, further work is needed to clarify the relationship between these variations and adaptive strategy of this species growing on suboptimal substrate and insect’s attraction.