Mesophilic mixed cultures commonly used in Cheddar cheese production contain a mix of Lactococcus lactis subspecies cremoris and subspecies lactis. To explore microbial diversity of Cheddar cheese starter mixtures, the community dynamics within nine undefined starter mixes were determined by 16S amplicon sequencing, shotgun metagenomics and L. lactis isolate whole genome sequencing. Each starter culture showed a distinctive major consensuses sequence based on 183 Lactococcus lactis species-specific markers. The genomes of 97 isolates of L. lactis subsp. cremoris were grouped into 7 clades and their functions were compared using RAST (Rapid Annotation using Subsystem Technology). Reddy differential agar was used to differentiate isolates between lactococcal subtypes, and those isolates were further classified for proteolytic and acidification performance. Isolates were grouped into categories of cremoris genotype cremoris phenotype (‘true cremoris’) and cremoris genotype lactis phenotype. This can help further explain the cremoris/lactis genotype and phenotype discrepancies of the Lactococcus lactis subspecies.