Externally visible, growing calcitic structures can be marked using fluorochromes. Such marks are useful for field recapture studies in ecology, evolution, and aquaculture as well as for studies on mechanisms of growth and development. We marked 2-month-old sea urchins (Strongylocentrotus droebachiensis) with the fluorochromes calcein, calcein blue, and tetracycline by batch-marking via immersion. Neither growth nor survival was affected by marking. Marks were externally visible on the skeletal plates, demipyramids, and spines of 100% of the marked sea urchins up to 63 d post-marking. After 342 d, marks were still externally visible on 100% of calcein-marked, 98% of calcein blue-marked, and 22% of tetracycline-marked sea urchins. Marks were brightest on calcein-marked and faintest on tetracycline-marked sea urchins, in correspondence to the fluorochrome dose. Growth marks in the aboral oculogenital ring, followed for 333 d, showed that genital plate growth in the hoop direction was greatest adjacent to the anal suture and that both the oculogenital ring and periproct grew less than isometrically. Internal marks (not externally visible) were subsequently seen on 99% of the demipyramids at 342 d post-marking. Such fluorochrome marks on demipyramids have previously been used to measure aboral and oral-end demipyramid growth to allometrically calibrate diametrical growth rates of field sea urchins. We found that although aboral demipyramid marks were always clear, 13% of marks on the oral end were obscured. However, we show that measuring only aboral end growth is sufficient for allometric calibration. In a separate experiment, multiple marks of the above three fluorochromes plus alizarin complexone, administered by injection to larger (12.9–37.1 mm diameter) sea urchins, persisted internally for at least 2 years. Multi-color, internally and externally visible, persistent marks will enhance experimental designs in laboratory, field, and common garden experiments.