The naphthalene dioxygenase (NDO) from Pseudomonas sp. Strain NCIB 9816-4 is a multicomponent enzyme system that carries out the initial step in the degradation of naphthalene. This enzyme has a broad substrate range and catalyzes several types of reactions including cis-hydroxylation, monooxygenation, and desaturation. In this study 1-phenylpyrazole and 1-phenylpyrrole were tested for biotransformation by NDO. HPLC analysis showed two metabolites from each substrate were produced by NDO. LC/MS analysis indicated the molecular weight of metabolites M1 and M2 of 1-phenylpyrazole were increased by 16 and 34 respectively which could be assumed as monooxygenation and dioxygenation reaction. On the other hand, HPLC and LC/MS analyses of metabolites M1 and M2 from 1-phenylpyrrole showed increased molecular weight of 16 and 32, as compared to the parent compounds, proposing addition of one and two atoms of oxygen to substrate, respectively. The structures of the metabolites were confirmed by 1HNMR and 13CNMR analysis.