Coffea arabica and Coffea canephora (Robusta coffee) are the most commonly consumed coffee varieties globally. In this contribution, NMR was used to confirm the coffee authenticity and LC-ESI-MSn technique was employed to profile and quantify the most abundant chlorogenic acid in 54 different samples of the two coffee varieties from diverse origins. Significant variations were observed for feruloyl quinic acids, dicaffeoyl quinic acids and 5-sinapoylquinic acid while the mono-caffeoyl quinic acids showed no variation when the two coffee varieties were compared. Additionally isomer ratios were explored as a potential marker for coffee authenticity along with a thorough statistical evaluation of rather extensive data set. Robusta 5-CQA when compared with 3,4-DiCQA Robusta shows high positive correlation, similar high correlation coefficient was observed in 5-pCoQA Robusta when compared with 3-pCoQA as against the Arabica.