Research on bioremediation of polycyclic aromatic hydrocarbons (PAHs) has established that several remediating microbial species are capable of degrading only low molecular weight (LMW)-PAHs, whereas high molecular weight (HMW)-PAHs are hardly degradable. In the present study, the efficiency of degradation of both LMW and HMW-PAHs by cytochrome P450 monooxygenase (CYP) of microalgae was studied. CYP have a key role in the detoxification of xenobiotics. So far, the structure of CYP in microalgae is not predicted; the protein structure was constructed by molecular modelling in the current study using the available template of microalgal CYP. Modelled microalgae 3D structures were docked against 38 different PAH compounds, and the information regarding the interaction between protein and PAHs viz. binding sites along with mode of interactions was investigated. We report that CYP from the microalgae Haematococcus pluvialis and Parachlorella kessleri was found to possess broad oxidising capability towards both LMW and HMW-PAHs. P. kessleri showed a least value with extra precision glide score of - 10.23 and glide energy of - 23.48 kcal/mol. PAHs bind to CYP active sites at Lys 69, Trp 96, Gln 397 and Arg 398 through intermolecular hydrogen bonding. Also, study revealed that PAHs interacted with CYP active sites through intermolecular hydrogen bonding, hydrophobic bonding, π-π interactions and van der waals interactions. Thus, structural elucidation study confirms that microalgae Parachlorella kessleri have the capacity to remediate HMW more efficiently than other microorganisms. Our results provide a framework in understanding the structure and the possible binding sites of CYP protein for degradation of PAH and that could be a screening tool in identifying the phycoremediation potential.