In situ skeletal markers have been widely used to quantify skeletal growth rates of scleractinian corals on sub-annual time-scales. Nevertheless, an evaluation of different techniques, both in terms of their efficacy and potential impacts on the growth process itself, has not been undertaken. Here the effects of exposure to four different dyes (alizarin, alizarin complexone, calcein, oxytetracycline) and isotope spikes (Ba and Sr) on the growth rates of scleractinian corals are compared. Oxytetracycline increased coral growth. Alizarin, alizarin complexone, calcein, and Sr and Ba isotope spikes had no significant effect on coral growth, but polyp extension appeared reduced during exposure to alizarin and alizarin complexone. Calcein provided a more intense fluorescent mark than either alizarin or alizarin complexone. Isotope spikes were challenging to locate using isotope ratio analysis techniques. Thus, calcein appears best suited for marking short-term calcification increments in corals, while a combination of alizarin or alizarin complexone and calcein may be useful for dual labeling experiments as there is little overlap in their fluorescence spectra.