The trace metal element zinc (Zn) participates in coral metabolic processes and therefore accumulates in their skeletons. These metabolic processes are largely controlled by the changes of environment in which they live, so Zn isotopic compositions (δ66Zn) in coral skeletons may possibly serve as potential tracers for climate and environmental changes. In this study, we first reported the δ66Zn in shallow‐water coral skeletons by investigating with monthly resolution δ66Zn values in the skeleton of a modern Porites coral 10AR2 from the Great Barrier Reef of Australia, and the bulk skeletal δ66Zn values of several coral species from the Luhuitou Reef of Hainan Island in the northern South China Sea. Correlations between δ66Zn and other climate and environmental proxies (Sr/Ca, δ18O, and δ13C) and instrumental environmental variables (sea surface temperature, river runoff, and chlorophyll a) are poor, suggesting that the effects of external environmental changes on monthly variations in δ66Zn in coral skeletons are not significant. However, significant interspecific differences in the skeletal δ66Zn of corals growing under identical external environments may suggest the occurrence of biologically controlled δ66Zn fractionation during coral skeletons formation. In addition, the monthly δ66Zn in the 10AR2 coral skeleton roughly decreases with increasing temperature, which is in agreement with the recent finding that δ66Zn in coral tissues and zooxanthellae increases with increasing temperature and can serve as a proxy for thermal stress in corals. We thus suggest that the complicated coral internal biological processes hinder the use of skeletal δ66Zn as a climate and environmental proxy. Plain Language Summary Zinc (Zn) is an essential micronutrient during the growth process of corals, and its contents in coral skeletons have been investigated for tracing the history of marine environmental pollution. However, the characteristics and potential applications of δ66Zn in coral skeletons have not been reported so far. In order to better understand the significance of δ66Zn in coral skeletons, we first investigated the monthly resolution δ66Zn values in the skeleton of a modern Porites coral from the Great Barrier Reef, and the bulk skeletal δ66Zn values of other shallow water coral species from the Hainan Island in the northern South China Sea. The results indicate that the changes of monthly δ66Zn values in coral skeletons may not be primarily controlled by external climate and environmental factors. The significant differences of skeletal δ66Zn values among different coral species imply that internal biological activities of coral holobiont play an important role in Zn isotopic fractionation in shallow‐water coral skeletons. In this regard, the application of δ66Zn in shallow water coral skeletons as a climate and environmental indicator is limited. Key Points The seasonal and bulk zinc (Zn) isotope compositions in shallow‐water coral skeletons were first reported The correlations between seasonal Zn isotope composition in coral skeletons and environmental variables are poor Interspecific differences in coral skeletal Zn isotope compositions suggest a biologically controlled fractionation process