Honey has a characteristic microbiological profile depending on their physical and chemical composition, results of the concentration sugar, with a high degree of resistance to the proliferation of microorganisms. Thus, the aim of the present study was to compare the morphophysiological and molecular methods for identification of yeast isolated from the honey obtained from the Apis mellifera L. bee. To this end, 97 samples of floral honey acquired at two of Piauí's, Brazil, honey cooperatives were analyzed. Yeast identification was conducted by the morphophysiological method and by the molecular analysis of the sequences of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region. Six yeast strains were isolated, two of them new isolated species; however comparisons between the morphophysiological and molecular methods showed divergence in the identification all the isolated species. Thus, it is concluded that morphophysiological identification tests alone are unreliable as a single yeast identification means and that molecular methods showed higher effectiveness in the identification of yeast isolates. © All Rights Reserved.