In an increasingly globalized world, extra virgin olive oil quality and authenticity is an important issue in order to assure consumer’s protection, prevent unfair competition and disrupt the national economy by a false declaration of origin. Hence, the recognition of EVOO authenticity is of great interest in terms of commercial and quality aspect. The objective of this study was to evaluate and discriminate monovarietal extra virgin olive oils of the two dominant olive cultivar, Lianolia Kerkyras and Koroneiki, produced in the coastline part of Western Greece, based on their chemical characteristics followed by statistical and chemometric analysis in order to identify possible markers for authenticity purpose. A total of 104 olive oil samples were collected. Both cultivars had an overall high quality profile as far as their basic qualitative parameters is concerned. Olive oils of cv. Koroneiki are characterized by a higher concentration in the mono-unsaturated oleic acid and the saturated stearic acid compared to cv. Lianolia Kerkyras, while a clearly higher concentration in the poly-unsaturated linoleic acid was observed in olive oils of cv. Lianolia Kerkyras. In addition, olive oil samples of cv. Koroneiki showed a clear lower total sterols concentration with a percentage of 40,9% not surpassing the required EU Regulatory limit of 1000 mg/kg, an observation which strengthens previous published results of our research group and depicts an overall “special characteristic” of cv. Koroneiki. As far as, the profile of the individual sterols is concerned, Lianolia Kekryras samples exhibited higher mean value for the major sterol, β-sitosterol and lower mean value for the rest most abundant sterols compared to the relative values of Koroneiki olive oils. Analysis of variance and principal component analysis of the GC- analyzed olive oil samples showed substantial compositional differences in their fatty acid and sterolic profile demonstrating a strong botanical effect, indicating those compositional markers as possible authenticity tools.