In the Inter-LINE (IL) PCR method, oligonucleotides GF, GR and 01, which originated from mammalian cells led to highly reproducible patterns of amplified template DNA, based on the consensus of LINE-sequences. These were used for the genomic fingerprinting of about 80 strains of yeast, consisting of 30 species from 13 genera). The IL-PCR technique using the above primers is described and compared to reference methods such as Arbitrarily Primed-PCR and Pulse Field Gel Electrophoresis (PFGE). A comparison of the two PCR variants was performed using suitable numbers of digitized PCR-fingerprints. A database for an automated yeast identification system is proposed.