The objective of this study was to determine the effects of incremental replacement of dietary linoleic acid by >20-carbon polyunsaturated fatty acids (PUFA) on changes in population of ruminal micro-organisms associated with fibre digestion and biohydrogenation using real-time PCR of bacterial 16S rRNA sequences. Four beef steers with ruminal cannulas were randomly assigned to control (CK, 65:35 forage to concentrate), CK with 3% sunflower oil plus 1% fish oil (S3F1), 2.5% sunflower oil plus 1.5% fish oil (S2.5F1.5) or 2% sunflower oil plus 2% fish oil (S2F2) in a 4 × 4 Latin square design with 21-day periods. Ruminal fluid was collected on day 15 of each period. Compared with CK, oil addition led to lower ruminal acetate and butyrate but greater propionate concentration. DNA copy number of Anaerovibrio lipolytica in ruminal fluid was greater with oil (average 5.38 vs. 3.62 × 105 DNA copy number), particularly with S2F2 relative to CK. Fibrobacter succinogenes and Butyrivibrio fibrisolvens DNA copy number decreased by 74% (1.06 vs. 4.01 × 105) and 39% (5.16 vs. 8.42 × 107) in response to S2F2 compared with CK. DNA copy numbers of Ruminococcus flavefaciens and Ruminococcus albus were not affected by incremental fish oil. Results suggest that greater availability of PUFA with >20 carbons (i.e. eicosapentaenoic acid and docosahexaenoic acid) promoted changes in bacterial populations that are relevant for fibre digestion and biohydrogenation.