We extend recent work on the analysis of synchronization in a pair of biochemical oscillators coupled by linear bulk diffusion, in order to explore the effects of discrete delays. More specifically, we consider two well-mixed, identical compartments located at either end of a bounded, one-dimensional domain. The compartments can exchange signaling molecules with the bulk domain, within which the signaling molecules undergo diffusion. The concentration of signaling molecules in each compartment is modeled by a delay differential equation (DDE), while the concentration in the bulk medium is modeled by a partial differential equation (PDE) for diffusion. Coupling in the resulting PDE–DDE system is via flux terms at the boundaries. Using linear stability analysis, numerical simulations and bifurcation analysis, we investigate the effect of diffusion on the onset of a supercritical Hopf bifurcation. The direction of the Hopf bifurcation is determined by numerical simulations and a winding number argument. Near a Hopf bifurcation point, we find that there are oscillations with two possible modes: in-phase and anti-phase. Moreover, the critical delay for oscillations to occur increases with the diffusion coefficient. Our numerical results suggest that the selection of the in-phase or anti-phase oscillation is sensitive to the diffusion coefficient, time delay and coupling strength. For slow diffusion and weak coupling both modes can coexist, while for fast diffusion and strong coupling, only one of the modes is dominant, depending on the explicit choice of DDE.