Scale surface microstructure of reptiles are multifarious. There are macro- and micro-structural features such as sharp spines, leaf-like microornamentation and pores. However, the argument on whether they indicate taxonomic relationship or convergent evolution is still open as well as their effect on wettability or dirt shedding. Here we show a comparison of scale microstructure in closely related Natrix natrix and Natrix tessellata which differ in ecological niches. We found marginal denticulations on the distal boundary of the Oberhäutchen cells and two types of micropores; Type I covers the surface of Oberhäutchen cells and Type II covers the epidermal folds of hinge regions. Type I micropores are longitudinal grooves on dorsal scale surface while they are rounded on the surface of the gastrosteges. Type II are similar both inter and intra-specifically. Our results are in line with previous studies that indicated an inverse ratio between pore number and wettability. We found no qualitative significance in terms of microstructural features. Our findings support the hypothesis saying that microornamentation is indicator of phylogenetic relations. Yet, only a few models of scale surface microstructure which are shaped by the environmental conditions could have been generalized which indicates that Oberhäutchen cells as simple elementary morphological structures are highly plastic and species-specific studies can be considered as special cases. Apart from contribution to an old “nature-nurture controversy”, we anticipate our assay to be a comparative perspective of the multifunctional integument of widely distributed Natrix sp.