Fish body muscles are arranged along the vertebral column in three-dimensional W-shaped blocks, called myomeres. Each myomere is separated from its neighbours by a collagenous sheet, the myoseptum, and embedded in these myosepta and in positions that are conserved throughout gnathostome evolution are distinct tendons. Within teleosts these tendons often ossify. Ossification is usually intramembranous but cartilaginous structures within the tendons have also been reported. Ossified myoseptal tendons are homologous to intermuscular bones and appear only in teleosts. The phylogenetic signal of myoseptal tendon ossfication has not been tested previously, although the presence and morphology of intermuscular bones have been used to infer phylogenetic relationships. We sample over a broad phylogenetic range of teleost fishes to test for (1) the effects of phylogenetic history on the presence of intermuscular bones and (2) morphological correlations with the presence of intermuscular bones. Body shape and fin position as well as vertebral number and aspect ratio are characters that are likely to affect the distribution of stresses along myoseptal tendons, and are therefore good functional predictors of myoseptal tendon ossification. We use the summary information by Patterson & Johnson for a list of species with intermuscular bones and reanalyse the homology of intermuscular bones to myoseptal tendons. We find that there is a phylogenetic signal in the distribution of four out of six ossified tendons, but that after correcting for phylogenetic relationships there are still morphological predictors for the presence of all ossified tendons. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106, 607–622.