Cobalt nanoparticles are incorporated into hexagonal honeycomb mesoporous silica to study the effect of nanoscale confinement on magnetic coupling. The superparamagnetic Co particles can fill a significant fraction of the total pore volume and can constitute up to 22.1 +/- 0.9% by mass of the composite. We find that Co particles form chains in the silica pores, which results in altered magnetic coupling. For example, coupling within chains of Co particles in pores produces a higher coercivity than the value found in either noninteracting or randomly aggregated particles. Remanence measurements also indicate that the Co nanoparticles form ferromagnetically coupled chains, thus converting the structural anisotropy of the silica host into magnetic anisotropy in the guest. This work demonstrates a method to create anisotropy in a nanoscale composite using easily synthesized isotropic building blocks.