This experiment aimed to determine the effects of camelina cake (CC) at different dietary fat levels on the ruminal bacterial community composition and how it relates to changes in ruminal fermentation and nutrient flow in a dual-flow continuous culture system. Diets were randomly assigned to 8 fermentors in a 2 × 2 factorial arrangement of treatments in a 4 × 4 Latin square design with four 10-d experimental periods that consisted of 7 d for diet adaptation and 3 d for sample collection. Treatments were (A) 7.7% CC inclusion at 5% ether extract (EE) (CC5); (B) no CC at 5% EE (NCC5); (C) 17.7% CC at 8% EE (CC8); and (D) no CC at 8% EE (NCC8). Diets contained 55% orchardgrass hay and 45% concentrate, and fermenters were fed 72 g of DM/d twice daily at 0800 and 2000 h. The bacterial community of each sample was determined by sequencing the V4 region of the 16S rRNA gene using the Illumina MiSeq platform. The most abundant phyla across treatments were Bacteroidetes and Firmicutes, accounting for 49% and 39% of total sequences, respectively. The bacterial community compositions in both of liquid and solid fractions of effluent digesta were changed (P < 0.01) by dietary CC but not by dietary fat levels. Including CC in the diets decreased (P < 0.05) the relative abundance of Ruminococcus flavefaciens, Ruminococcus albus, Fibrobacter spp., and Butyrivibrio spp. The most abundant genus, across treatments, Prevotella, was decreased (P < 0.05) by high dietary fat levels while Megasphaera was increased (P < 0.01) by CC in the liquid fraction. Correlatively, the concentration of acetate was decreased (P < 0.01) while propionate was increased (P = 0.01); saturated fatty acid (C16:0 and C18:0) were decreased (P < 0.01) and PUFA, especially C18:2 n-6 and C18:3 n-3 were increased (P < 0.01) by dietary CC. Based on the correlation analysis between genus and metabolites, this study revealed that CC could be energetically beneficial to dairy cows and useful at suppressing ruminal bacteria associated with biohydrogenation; however, attention should be given to avoid negative effects of CC on suppressing cellulolytic bacteria.