We consider a tight-binding model with the nearest neighbour hopping integrals on the honeycomb lattice in a magnetic field. Assuming one of the three hopping integrals, which we denote t a , can take a different value from the two others, we study quantum phase structures controlled by the anisotropy of the honeycomb lattice. For weak and strong t a regions, respectively, the Hall conductances are calculated algebraically by using the Diophantine equation. Except for a few specific gaps, we completely determine the Hall conductances in these two regions including those for subband gaps. In a weak magnetic field, it is found that the weak t a region shows the unconventional quantization of the Hall conductance, σ xy = −(e 2 /h)(2n + 1), (n = 0, ±1, ±2, · · · ), near the half-filling, while the strong t a region shows only the conventional one, σ xy = −(e 2 /h)n, (n = 0, 1, 2, · · · ). From topological nature of the Hall conductance, the existence of gap closing points and quantum phase transitions in the intermediate t a region are concluded. We also study numerically the quantum phase structure in detail, and find that even when t a = 1, namely in graphene case, the system is in the weak t a phase except when the Fermi energy is located near the van Hove singularity or the lower and upper edges of the spectrum.