The aim of this study was to evaluate the bacterial ecosystem of milk and Ezine cheese by PCR amplification of the V3 region of the bacterial 16S rRNA gene followed by denaturing gradient gel electrophoresis (DGGE) and by monitoring the bacterial diversity dynamics using PCR single-strand conformation polymorphism (SSCP) analysis. PCR-DGGE analysis revealed that 17 different bands and strains belonging to the Lactococcus lactis group and Streptococcus thermophilus were predominant during manufacturing and ripening. SSCP analysis revealed that the bacterial profiles of the two cheese samples were similar.