This dataset contains measurements of oxygen uptake rates, histological morphometrics, and immunoreactive cell metrics in Acanthochromis polyacanthus and Amphiprion melanopus throughout their embryonic development. Data includes: histological morphometrics (i.e., structure becomes apparent), oxygen uptake rates (eaverage oxygen uptake rates), immunoreactive density data (yolksac and trunk), immunoreactive cell size data (yolksac and trunk), and immunoreactive gill density (density estimates).