A search for narrow vector resonances decaying into quark-antiquark pairs is presented. The analysis is based on data collected in proton-proton collisions at s=13 TeV with the CMS detector at the LHC, corresponding to an integrated luminosity of 35.9 fb−1. The hypothetical resonance is produced with sufficiently high transverse momentum that its decay products are merged into a single jet with two-prong substructure. A signal would be identified as a peak over a smoothly falling background in the distribution of the invariant mass of the jet, using novel jet substructure techniques. No evidence for such a resonance is observed within the mass range of 50-300 GeV. Upper limits at 95% confidence level are set on the production cross section, and presented in a mass-coupling parameter space. The limits further constrain simplified models of dark matter production involving a mediator interacting between quarks and dark matter particles through a vector or axial-vector current. In the framework of these models, the results are the most sensitive to date, extending for the first time the search region to masses below 100 GeV.[Figure not available: see fulltext.].