35 physico-chemical descriptors were used to characterize all 75 congeners of chloronaphthalene in terms of their environmental stability and specific dioxin-like toxicity. A prepared basic thermodynamic and physico-chemical property data matrix of PCNs was interpreted using Principal Component Analysis (PCA). The PCA of the thermodynamic and physico-chemical data matrix created a four-dimensional model that explained 76% (58% + 9% + 5% + 4%) of the total variance. The loading plot shows that the first PC is influenced by variables describing degree of chlorination, molecular weight, polarizability and lipophilicity. The best positively correlated descriptors are: retention time, standard molar entropy, heat capacity, a first-order molecular connectivity index, logarithm of octanol-water partition coefficient, the Wiener Index, specific polarizability, a third order shape index for molecules, the sum of absolute of the charges on each atom of the molecule, molecular weight, polarizability, refractivity, solvent-accessible surface, van der Waals surface, solvent-accessible volume, van der Waals volume. Negatively correlated descriptors are: standard enthalpy of formation and energy of HOMO. The second PC is strongly influenced by energy of LUMO, while substitution pattern parameters, number of chlorine atoms at a-positions and vicinal (adjacent) carbon atoms substitution pattern are less important parameters. The third PC depends on dipole moment and the largest negative charge, and on substitution at position 2 of naphthalene nuclei, while the symmetry group parameter is determined by PC4. There are small groups consisting of compounds which have similar values of LUMO energy and substitution pattern. The congeners of CN substituted with chlorine at positions 1, 2, 3, 6 and 7 (Fv/Fv PCN congeners), and next those substituted at positions 1, 2, 3 and 6 or 7 (Fr/Fv PCB congeners) are considered to be most potent in terms of dioxin-like toxicity, and followed by those substituted at four positions (Fr[Fv), at three positions (Tr/Fv) and so on. The thermodynamic stability of the congeners of CN depends on the number of attached chlorine and structure of the molecule. Among the 75 congeners of CN only a few, like PCN nos. 42, 560, 61, 66/67, are relatively resistant to biodegradation and biomagnify in animals occupying a higher position in the marine food web, and with a particular homologue group they are characterised by the lowest absolute values of energy of LUMO.