Rapidly rotating atomic gases provide a platform for studying phenomena akin to type-II superconductors and quantum Hall systems. Recently, these systems have attracted renewed interest due to technological advances in the trap anisotropy control, in-situ observation capabilities, and cooling and rotating complex atomic species such as dipolar gases. Understanding the vortex lattice formation and quantum melting is crucial for exploring quantum Hall physics in these systems. In this paper, we theoretically investigate the vortex lattices in anisotropic quantum gases. We formulate the rotating gas Hamiltonian in the Landau gauge, and consider the effects of additional perturbations such as the trap potential in the lowest Landau level (LLL). Focusing on the gases with short-range interactions, we obtain the many-body Hamiltonian projected to lowest Landau level. We consider the limit of full Bose-Einstein condensation and obtain the governing Gross-Pitaevskii equation to identify the possible vortex phases. We numerically solve the Gross-Pitaevskii equation using the imaginary time evolution, and demonstrate the possible vortex lattices as a function of anisotropy, rotation speed and interaction strength. We show that the number of states with a support in the LLL, which determines the number of vortices, follows a Thomas-Fermi type scaling albeit with slightly different coefficients from the usual condensates.