Yeast populations on 24 lots of Spanish fermented sausages, made by four factories (F1, F2 and F4, artisanal; F3, industrial) were investigated throughout manufacture and the influence of different variables evaluated. In addition, 41 yeast strains were identified at the species level using two miniaturised systems: ATB32C (API System) and Vitek Yeast Biochemical Card (Vitek YBC). Levels of yeasts found in the sausage mixture (mean counts around 4 log units/g) were similar to those described by other authors. In sausages from factories F1 and F2, a further increase was noted, reaching 5.5 log units/g after fermentation. Counts subsequently decreased to 3.6 and 5 log units/g, respectively. In sausages from factories F3 and F4, decreasing counts were observed from the beginning, particularly in sausages from F3, where yeasts were almost absent in the finished product. Type of manufacture and sausage diameter, were the variables most influencing yeast counts. Debaryomyces hansenii (teleomorph of C. famata) was the dominant species, being found at all stages of manufacture. Trichosporon ovoides (formerly T. beigelii), Yarrowia lipolytica (perfect form of C. lipolytica), C. intermedia/curvata, C. parapsilosis, C. zeylanoides and Citeromyces matritensis (teleomorph of C. globosa) were also present. Direct identification was possible only with 50% of the total of strains investigated, although a higher number of strains was identified using the API than the Vitek YBC system.