The importance of microbes for the functioning of oceanic food webs is well established, but their relevance for top consumers is still poorly appreciated. Large differences in individual size, and consequently in growth rates and the relevant spatial and temporal scales involved, make the integration of microorganisms and large metazoans in a common food web framework difficult. Using stable isotopes, this study estimated the trophic position of 13 species of micronektonic fishes to examine the microbial and metazoan contribution to mid trophic level consumers. Vertically migrant species displayed higher trophic positions than non-migrant species in all depth layers. The estimated trophic positions agreed well with those from the literature, but all species displayed mean increases between 0.5 and 0.8 trophic positions when taking into account microbial trophic steps. Trophic position, but not the relative importance of the microbial food web, increased with individual size, suggesting that current estimates of the trophic position of top consumers and of the length of oceanic food webs are too low because they are based only on metazoan trophic steps. This finding calls for a review of trophic position estimates and of the efficiency of trophic transfers along oceanic food webs.