Rumen bacteria form a dynamic, complex symbiotic relationship with their host, degrading fibrous forages to provide volatile fatty acids (VFA) as energy to the animal. The objective of this study was to characterize rumen bacteria and VFA in 3 breeds of primiparous dairy cattle, Holstein (HO, n = 7), Jersey (JE, n = 8), and HO x JE crossbred (CB, n = 7), at early (3 DIM) and peak lactation (93 DIM). All cows were fed a consistent TMR at a 70:30 forage to concentrate ratio. Rumen digesta were collected via esophageal intubation at 3 and 93 DIM. Microbial DNA was extracted and sequenced using Illumina MiSeq (v. 3) following PCR amplification of the V1-V3 region of the 16S rRNA gene. Sequences were analyzed using Mothur. The 16S copy numbers of rumen bacterial densities were quantified by real-time PCR. Data were analyzed using a repeated measures general linear mixed model in SAS. Breed (B) had no effect on rumen VFA, however, molar concentrations of acetate, butyrate, and propionate were lower at 93 DIM (74.7, 10.7, and 20.8 mM, respectively) than at 3 DIM (93.8, 14.7, and 26.9 mM, respectively; P < 0.01). The quantity of bacteria in rumen digesta was unaffected by B or lactation stage (LS). Overall, Bacteroidetes (Bd) was the predominant phylum, accounting for 54–78% of total bacteria, followed by the phyla Firmicutes (Fc; 19–42%) and Proteobacteria (1–4%). Prevotella was the predominant genus of the Bd phylum and was unaffected by B, however, Prevotella species did increased with LS (49.8% vs. 67.3% for 3 DIM and 93 DIM, respectively; P < 0.01). At 93 DIM there was a lower abundance of Fc (38.5%) than at 3 DIM (25.0%; P < 0.01), with bacteria belonging to the genera Butyrivibrio and Coporococcus decreasing from 3 DIM (1.74% and 1.33%) to 93 DIM (0.26% and 0.30%; P < 0.01). Bacteria belonging to the genera Mogibacterium and Ruminoccocus within the Fc phylum were affected by B (P < 0.05), HO had less Mogibacterium species than CB and JE (0.58% vs. 1.22% and 1.26%), and HO had higher abundance of Ruminoccocus species than CB and JE (2.3% vs. 1.5% and 1.3%; P < 0.05). In conclusion, LS had a greater effect on bacterial communities and VFA than host genetics.