The contents of eight trace elements (Ti, Mn, Ni, Cu, Zn, Sr, Ba, and Pb) in muscles of syntopic sexual and clonal spined loaches (the golden loach Sabanejewia baltica, diploid males and females of Cobitis taenia, and congeneric triploid clonal females) from the upper Dnieper River and in the syntopic spined loaches (males and females of C. melanoleuca and males of C. taenia) from the upper Volga River basin were determined using the X-ray fluorescence spectroscopy technique. The contents of Cu in the clonal triploid Cobitis females and diploid C. taenia females from the Dnieper are different. The intersexual differences in the contents of Pb and Zn between C. taenia males and females, as well as the interspecific differences in the content of Ti between the spined loaches from the Dnieper and Volga basins were revealed. The concentrations of Cu and Pb correlated with the individual fish size. The potential for the use of the revealed differences in the trace element contents as an indicator of the divergence of ecological niches in the syntopic spined loaches is discussed.