Embryos of the annual killifish Austrofundulus limnaeus have a remarkable tolerance to anoxia during their development, especially during diapause II (DII), but little is known about potential mechanisms by which this tolerance is achieved. This study examined the aerobic and anaerobic capacities of these embryos as they develop along alternate developmental trajectories and in response to altered incubation temperature. Aerobic and anaerobic capacities were estimated by measuring the total activity of the enzymes citrate synthase (CS) and lactate dehydrogenase (LDH), respectively. Embryos of A. limnaeus exhibit high anaerobic capacity throughout development as evidenced by high LDH/CS ratios, especially during early development through DII. Anaerobic production of lactate is supported by the heart isoform of LDH, even in stages of development that exhibit extreme tolerance of anoxia. CS capacity is extremely low during DII and may indicate an active suppression of mitochondrial metabolism during this stage of dormancy. Post-DII and "escape" embryos which bypass DII increase their aerobic and anaerobic capacities in tandem as they develop. The activity of both LDH and CS continue to increase for many days after morphological development ceases during DIII. Based on this observation, it is likely that regulation of metabolic dormancy is different in DII and III. Escape embryos seem to develop along a different metabolic trajectory than do embryos that enter diapause. Importantly, these embryos complete development with different enzymatic capacities that could influence physiological and ecological performance during early larval life.