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One of the goals for strong field physics is imaging the dynamics of the quantum systems, and in case of molecules, there is strong interest in imaging of the electron rearrangement during chemical reactions. Strong field ionization of molecules has many attractive features that make this process a candidate tool for strong field imaging of transient states and chemical reactions. In this paper, we present analysis of ionization dependence on orientation of molecular axis with respect to polarization of the electric field of the laser. By considering several examples of molecules at their equilibrium internuclear distances and an example of the simplest chemical reaction, namely, the dissociation of diatomic molecule, we present how symmetries of the molecular orbitals influence the alignment-dependent ionization and how this dependence can be used to follow molecular dynamics using strong field multiphoton ionization.