Aims: This study investigates the dynamics of the microflora, particularly the lactobacilli, in Cheddar cheese manufactured from raw and microfiltered milk containing different adjunct cultures. Methods and Results: Sixteen cheeses - raw milk, adjunct and control cheeses - were manufactured in four trials. Lactobacilli were identified by PCR methods in one trial, and by phenotypic typing for all trials. Numbers of lactobacilli were significantly different at day 1 and 3 months in the control and adjunct-containing cheeses. In the raw milk cheeses, Lactobacillus paracasei was detected throughout ripening, Lact. curvatus at the end, and Lact. plantarum at day 1 only. Lactobacillus strain diversity decreased from raw, control to adjunct cheeses. Enteroccoci and coliform numbers further differentiated raw cheeses from the others. Lactococcal starter numbers also differed in the three cheese types and differences were observed within adjunct cheeses. Although adjunct lactobacilli dominated in the cheese to which they were added, strains with similar phenotypic profiles were also detected on occasions in some of the control cheeses. Conclusions: The addition of adjunct lactobacilli modified the growth kinetics of both adventitious lactobacilli and starter lactococci during ripening. Appropriate strain tracking is necessary to monitor changes in the population profiles of control and experimental cheeses in trials utilizing adjunct cultures. Significance and Impact of the Study: Investigations of the role of adjunct strain(s) in cheeses may be complicated by the interactions between the adjunct and the other cheese strains, and effective strain monitoring by genotypic or phenotypic methods is essential if valid comparisons are to be made.