The study aimed to describe the interactions between nutrition and caecal bacteria abundance using odd-numbered and branched-chain fatty acids (OBCFA). Following a 2 × 2 factorial design, 47 rabbits were fed diets with two levels of digestible fibre (DF, 180 vs. 260 g/kg DM) supplemented with soybean oil (SO, 20 g/kg) or not. At 77 days of age, fatty acid (FA) composition was determined in caecal contents. The microbial origin of OBCFA vs. dietary FA in caecal contents was illustrated by clustering of these FA in the loading plots of principal component analysis. The contribution of odd-numbered FA in the OBCFA pattern was increased (p < 0.05) for high DF diets, whereas that of branched-chain FA decreased (p < 0.05), indicating potential shifts in the relative abundance of Gram-negative and Gram-positive fibrolytic bacteria respectively. Soybean oil reduced the relative importance of OBCFA (p < 0.001) in total microbial FA; however, its effects appeared to depend on the readily available fermentable substrate, as indicated by the DF × SO interactions (p < 0.001). In conclusion, OBCFA may be potentially used as markers of caecum function, but further detailed studies are necessary to validate their use as diagnostic tools in rabbit nutrition.