Annulus counts were compared between four sectioned levels of first dorsal-fin spines (D1–6) and anal-fin spines (A1–3) of Striped Marlin (Kajikia audax) caught in the southwest Pacific Ocean. The number of annuli observed in transverse sections varied significantly between spines of individual fish and between sections cut at varying distances along spines. Sections at levels ¼ and 1 condyle width (CW) of spines D4–6 and A3 displayed the greatest number of annuli and were not significantly different from one another. Pending validation of yearly periodicity of annulus formation, these sections could be used interchangeably in future age and growth studies on this species. The percentage of bone remodelling (vascularization) present within the central portion of fin-spine sections was negatively correlated with annulus counts. Vascularization affected the visibility of early formed annuli, which resulted in reduced counts and therefore ‘age’ estimates. Annulus counts were reduced in fin-spines D1–3, A1–2, and in sections from 2 CW and 3 CW in most spines. Statistical replacement techniques for annulus loss due to vascularization effectively nullified the differences observed between sections. This study demonstrated that annulus counts and subsequent ‘age’ estimates may vary significantly within and among calcified structures of individual fish. The risk of intra-structural variation is of particular concern to aging studies focused on species that are affected by vascularization, or where calcified structures are used indiscriminately.