In this investigation, we explored the oenological significance of Candida zemplinina (syn. Starmerella bacillaris) isolates from Apulian grape musts. Moreover, we provide the first evidence of the impact of different C. zemplinina strains on the wine aromatic properties tested as monocultures. We described the diversity of C. zemplinina strains isolated from grapes and the variability of ‘volatile’ phenotypes associated with this intraspecific variability. Thirty-three isolates were characterized at strain level by PCR-based approach and, among these, 16 strains were identified and then tested by microfermentation tests carried out in grape must. Analyzed strains were low producers of acetic acid and hydrogen sulphide, not able to decarboxylate a panel of representative amino acids, whereas they showed fructophilic character and significant glycerol production. Volatile profiles of produced wines were investigated by gas chromatography–mass spectrometry. The Odor Activity Values of all molecules were calculated and 12 compounds showed values above their odor thresholds. Two selected strains (35NC1 and 15PR1) could be considered as possible starter cultures since they were able to positively affect the sensory properties of obtained wine. This report firstly supplies evidence on the strain-specific impact of different C. zemplinina strains on the final aroma of produced wines.