We consider the influence of potential quark matter existing at high densities in neutron star (NS) interiors on gravitational waves (GWs) emitted in a binary NS merger event. Two types of equations of state (EoSs) at zero temperature are used - one describing pure nuclear matter and the other nuclear matter with a phase transition to quark matter at very high densities. Binary equilibrium sequences close to the innermost stable circular orbit (ISCO) are calculated to determine the GW frequencies just before the merger. It is found that the effects of the EoSs begin to play a role when gravitational masses are larger than M∞≃ 1.5 M⊙. The difference in the GW frequency at the ISCO increases by up to ≃10 per cent for the maximum mass permitted by the EoSs. We then perform three-dimensional hydrodynamic simulations for each EoS while varying the initial mass and determine the characteristic GW frequencies of the merger remnant. The implications of the presence of quark matter show up mainly in the collapse behaviour of the merger remnant. If the collapse does not take place immediately after the merger, we find a phase difference between the two EoSs in the post-merger GW signal. We also compare the GW frequencies emitted by the remnant of the merger to values obtained from simulations using a polytropic EoS and find an imprint of the non-constant adiabatic index of our EoSs. All calculations are based on the conformally flat approximation to general relativity and the GW signal from the merger simulation is extracted up to quadrupole orde
