In this research work first time different colorful varieties (Dark purple, light purple, white, yellow with different shape) of Solanum melongena has been selected to evaluate the intraspecific taxonomic confusions existing to classify the lower order taxa with the help of leaf epidermal anatomical markers. There are many taxonomic confusions were existed due to wide range of adaptability in different environmental conditions. This approach also assists to determine either the different shapes of leaf margins effect on the internal anatomy of long and round fruits of S. melongena. It also provided the similarities and dissimilarities among the related species, but does not provide sufficient knowledge to delaminate the lower order taxa. This approach also leads to choose the other chemical methodology after preliminary evaluation because many characters were same so for careful study and classification we need other genetically and chemical approaches.