<p>Coral restoration practitioners who maintain in-water nurseries measure phenotypic traits to identify colonies with the greatest chance of survival after transplantation to the reef, but these traits often exhibit high variation. Given the shared environmental conditions within nurseries, most of this variation can be attributed to host and symbiont genetics. It remains unclear how interactions between hosts and symbionts at the level of intraspecific genotypes shape holobiont performance. Here, we measured colony growth rates among different genotypic combinations of coral host (<i>Acropora cervicornis</i>) and microalgal symbiont (<i>Symbiodinium </i>“<i>fitti” nomen nudum</i>) reared in a common garden in-water nursery to explore the physiological consequences of genotypic interactions among partners. Host and symbiont genotype effects were difficult to detect owing to high variation and low replication, emphasizing the need for improved sampling designs. DNA sequencing also revealed an insufficient distribution of diversity to resolve interactive effects, exposing an additional challenge with using staghorn coral nurseries in this context. We propose that more easily manipulated symbiosis models, such as the Aiptasia sea anemone system, are better suited to investigate the consequences of genotypic interactions among cnidarian-dinoflagellate associations.</p>