The aim of this study was application of mid-IR spectroscopy in combination with multivariate statistical analysis for characterization of yeasts from two fermented products, wine and olive, in comparison with cultural and molecular tests and characterization of antimicrobial effects induced by olive phenolics on yeasts. Totally 19 wine yeasts were molecularly identified as M. pulcherrima (11%), P. membranifaciens (16%), H. uvarum (5%) and S. cerevisiae (68%). According to FTIR spectroscopic data of wine samples, S. cerevisiae isolates formed a cluster which were generally separated from all other yeasts. Totally 182 olive yeasts were identified from naturally debittered Hurma and a common olive variety and their leaves. The most common yeasts were Metschnikowia sp. (39%) and Aureobasidium sp (78%) in the first and the second harvest years, respectively. Since only Aureobasidium sp. was the common yeast isolated from Hurma during both years, any link between natural debittering of Hurma and the yeast population of this olive type might be related to Aureobasidium sp. Molecularly identified yeast types generally formed different clusters and showed spectral differences. For antimicrobial activity tests, all phenolic compounds were found effective on both S. cerevisiae and A. pullulans; however, A. pullulans was observed to be more sensitive. Antimicrobial activity was differentiated with respect to treatment time and phenol concentration with statistical treatment of FTIR data. As a complementary technique, FTIR could be successfully used for identification of yeasts and characterization of antimicrobial activity of phenolics against yeasts.