The molecular characterization of 14 strains of Kluyveromyces marxianus isolated from Agave fourcroydes (Lem.) in Yucatan, Mexico, was performed by AP-PCR analysis, PCR-RFLP of 5.8S-ITS, and complete NTS regions. A sequence analysis of the D1/D2 domain of the 26S rDNA was also carried out in six selected strains. The AP-PCR approach had the highest discrimination power for the molecular characterization of new henequen K. marxianus strains. PCR-RFLP of 5.8S-ITS regions did not reveal polymorphisms in this group of strains. The restriction enzyme digestion analysis of NTS region enables the separation among strains which coincides with ascospore shape groups. The molecular tools used in this article may be useful to confirm a preliminary screen of yeasts isolated from henequen without the use of growth characteristics or morpho-physiological tests.