Melanism is a polymorphic phenotype caused by the number and density of melanocyte cells producing melanin pigment in the skin and widely observed in snakes. The frequency of this coloration in populations is associated with its opposing fitness consequences and can be closely related to species-specific characteristics such as sex, reproduction, and nutrition, as well as environmental factors such as climate and geography. Although melanism is frequently seen in snakes, the skin structure of melanistic individuals has not been studied in detail. Also, the impact of the black phenotype on habitat use has not yet been clarified in this species. Here, we show a comparison of typical and melanistic morphs of the grass snake Natrix natrix population of Anatolia for the first time in terms of skin structure, habitat, and sex. We found that melanistic individuals, in which partial melanism is more abundant than total melanism, comprise 13% of the population. Melanocyte area of the skin is 1.4 times greater in melanistic compared to the typical individuals. The epidermis is thicker in typical morphs by 7.7%. Hinge regions between adjacent scales do not bare melanocytes in both morphs. As for habitat utilization, we revealed that melanistic individuals of the Isikli population tend to occur closer to water bodies than typical ones. Our data provide a new perspective on poorly known aspects of color polymorphism and habitat use of widely distributed, semi-aquatic Natrix natrix.