Gut microbiota profiles can be regarded as complex polygenic traits, that are influenced by both the host and the environment. The aim of the present study was to use microbial and genetic relationships to predict feed efficiency related traits (feed intake, body weight gain and feed conversion ratio) in pigs. Data were collected from 538 threeway crossbreed male grower-finisher pigs, all being genotyped at 50k SNPs. The pigs were fed ad libitum according to a three-phase feeding program with commercial diets based on wheat, barley and by-products. On the day before slaughter (mean body weight 125 kg) fresh faecal samples were collected per animal and sequenced for the 16S hypervariable region of bacteria (V3/V4) to profile the faecal microbiome, resulting in 2,276 operational taxonomic units after filtering. Using these data we calculated the proportion of variance in feed efficiency related traits explained by variation in the faecal microbiome, i.e. the ‘microbiability’, and genetic background, i.e. ‘heritability’. The microbiability values were 42% for average daily gain, 33% for average daily feed intake, and 46% for feed conversion ratio, whereas heritability values were 24, 39 and 22% respectively. Using leave-one-out cross-validation, we estimated the accuracy of prediction based on the microbiome profile and genotype of the pigs. The faecal microbiome profile had a stronger relationship with variation in average daily gain and feed conversion ratio than data on the genotype of the pig, while the opposite was observed for average daily feed intake. In conclusion, combining information on the genotype of the pig and its faecal microbiota composition could likely improve the accuracy of prediction of phenotypes for feed efficiency related traits.