Chemical markers in otoliths have been used to assess the stock structure of many marine fishes, but these natural markers have yet to be widely evaluated in the spines of sturgeon fishes in the Caspian Sea, which has six endangered sturgeon species. We used inductively coupled plasma mass spectrometry to quantify B, Ba, Ca, Cu, Fe, Li, Mg, Mn, Si, Sr, and Zn in pectoral fin spines of starry sturgeon (Acipenser stellatus) in the northern and southern Caspian Sea, where depth, salinity, and temperature vary from north to south. Fin spines showed significant regional differences in B/Ca, Cu/Ca, Mn/Ca, Si/Ca, Sr/Ca, and Zn/Ca (Scheirer–Ray–Hare test, p < 0.05). Principal component analysis indicated distinct north/south groups when considering all significant elements in ratio to calcium. The centroids of these regional groups differed significantly (PERMANOVA, p < 0.05). Flexible discriminant analysis classified 85.3% of fish into their correct regions using all element-to-calcium ratios. These results suggest that individuals in different regions share common lifetime environmental histories and may represent unique stocks in the Caspian Sea. Moreover, the findings suggest that pectoral fin-spine microchemistry can be used to identify stocks of starry sturgeon, thus providing a non-lethal approach to elucidating life-history details that are critical to the comprehensive management of sturgeon resources.