The lactic acid bacteria (LAB) and yeast diversities in spontaneously fermented pearl millet (Pennisetum glaucum) and finger millet (Eleusine coracona) sourdoughs were investigated. Pearl and finger millet grains were processed into flour and used in spontaneous sourdough fermentation. LAB and yeast cultures were isolated, screened and identified based on morphological, biochemical and sugar utilisation pattern using API 50CHL and API 20 AUX kits. Titratable acidity, pH and Temperatures of sourdoughs developed were also monitored. Titratable acidity and Temperature increased with increasing days of fermentation and conversely the pH. and mesophilic bacterial count followed that of a normal bacterial growth curve. Dominant LAB and yeasts in pearl and finger millet spontaneously developed sourdoughs were Lb. plantarum, Lb. plantarum 1, Pediococcus pentosaseus, Lb. pentosus, and Saccharomyces cereviasiae. However, Candida milleri was found in pearl millet sourdoughs. The dominant cultures in millet sourdoughs could find applications as starter cultures if improved sourdough quality is desired.