Abstract Bacteria generally ferment milk but, sometimes, yeasts are found in fermented milks. The presence of these yeasts in the microbial community of some fermented milks could be intentional or accidental. The Diversity of yeasts in the products was investigated using a molecular technique employing variable regions of 26S rDNA profiles generated by PCR-DGGE (Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis). Two types of samples: artisanal or handcraft yoghurt and traditionally fermented milks were collected in three towns of the three regions of the northern part of Cameroon. Firstly, a comparison was made between the 16 traditionally fermented milks collected in Maroua, Garoua and Ngaoundre each of the 3 regions. Secondly, it was between 26 artisanal fermented milks of each region and finally, between the two types of products. The different PCR-DGGE 26S rDNA profiles obtained were analyzed and DNA sequencing was used to compare yeasts from each method of production. Twelve (12) species of Yeasts were identified as: Malassezia globosa, Hanseniaspora uvarum, Galactomyces candidum, Candida tropicalis, Aureobasidium pullulans, Torulaspora globosa, Saccharomyces cerevisiae/paradoxus, Pichia kluyveri, Candida parapsilosis, Torulaspora delbrueckii, Kluyveromyces marxianus, Candida orthopsilosis and Pseudozyma sp. Yeast diversity was higher for artisanal fermented milks (yoghurt) with at least 10 species, while for traditionally non packed fermented milks only 5 species were identified with a predominance strain of Galactomyces candidum, Candida parapsilosis, Torulaspora delbrueckii, Saccharomyces cerevisiae/paradoxus and Kluyveromyces marxianus. The different species of yeast might be introduced accidentally in artisanal yoghurt; however, for traditionally fermented milks their presence might be associated to the starter.