Abstract Background The research was carried out to assess the lipid characteristics of oil extracted from the head and gills of Claris macrocephalus and Scomber scombrus. Results The results confirmed the presence of C16:0, C18:0, C18:1, C18:2, C18:3, C22:6 as the major fatty acids. Titus fish head (TFHD) oil had a total saturated fatty acid (TSFA) of 40.804 ± 0.002% of which C16:0 and C18:0 were the most dominant fatty acids present while the total monounsaturated fatty (TMUFA) acids present in the oil was 33.853 ± 0.001%. The total polyunsaturated fatty acid (TPUFA) content of the TFHD oil sample was found to be 25.368 ± 0.002%. The results revealed that the total unsaturated fatty acid (TUFA) present in the TFHD was higher than the TSFA. The results obtained for Titus fish gills (TFGL) oil sample followed the same trend as observed in the head sample. The results showed that the four (4) oil samples contain high level of palmitic acid (C16:0) and stearic acid (C18:0) both of which are saturated fatty acids (SFA). The main MUFA identified was C18:1 (cis-6) and ranged from 14.120 ± 0.004 to 20.418 ± 0.002% for TFHD, TFGL, CFHD, CFGL and oleic acid (C18:1) ranged from 10.297 ± 0.001 to 11.570 ± 0.003% for TFHD, TFGL, CFHD and CFGL. Conclusions Oils of CFHD and TFHD showed higher peroxide values indicating suitability for human consumption.