Rumen methanogens are anaerobic, methane-producing archaea that decrease feed efficiency in dairy cattle and contribute to global warming. The objective of this study was to determine if breed or lactation stage affect the rumen methanogen diversity and density. Seven Holstein (H), 8 Jersey (J), and 7 Holstein-Jersey crossbreeds (X) were co-housed in a free stall on a total mixed ration, and whole rumen digesta samples were collected at 3, 93, 183, and 273 d in milk (DIM). To determine the methanogen diversity, the V1-V3 region of the 16S rRNA gene was amplified. Sequences were generated using Illumina MiSeq v.3 and all bioinformatics analyses were performed using Mothur. Real-time PCR amplified the methanogen-specific mcrA gene and the mcrA copy numbers per mL rumen digesta were calculated. Data were analyzed using PROC MIXED in SAS. The model included the effects of breed (B), lactation stage (LS), and B x LS. A total of 1,683,569 16S sequence reads were classified to species-level taxa by B and LS. The Methanobrevibacter (Mbr.) smithii-gottschalkii-millerae-thaueri and Mbr. ruminantium-olleyae clades did not differ. Notably, the mean % abundance of the species Mbr. thaueri differed (P < 0.01) by LS. At 93 DIM, Mbr. thaueri abundance was higher in J (35.0%) compared with both H (24.5%, P < 0.05) and X (19.4%, P < 0.01), while no significance was observed at 183 and 273 DIM, respectively. Differences by LS were seen in less abundant species (<5%), Mbr. woesei (P < 0.001), gottschalkii (P < 0.05), millerae (P < 0.05), and Methanosphaera stadtmanae (P < 0.01). The top operational taxonomic units (OTU) from a 2% cutoff were related to Mbr. smithii, Mbr. thaueri, Mbr. ruminantium, and Mbr. millerae. There were no differences in methanogen density, the number of OTUs (18–37 per breed), or Shannon and Inverse Simpson indices. Chao values differed by LS (P < 0.01). Our data suggest that LS may have had a greater effect on the methanogen diversity than B and that core rumen methanogens persist over a lactation period.