Many species of fish eggs are spherical, transparent, about the same size and hence visually (“morphologically”) difficult, if not impossible, to correctly identify. This project is making use of advances in molecular genetics and sequencing technologies to explore new methods for efficient identification of fish eggs in environmental samples. The scientists have demonstrated the ability to use a PCR-based fluorescent probe array (developed in an earlier Sea Grant project) to identify fish eggs and larvae in archived ichthyoplankton samples collected during CalCOFI cruises. This work has shown that fish eggs are often misidentified. Pacific halibut, sand dabs and other flatfish are examples of a group of fish eggs that are easily confused. The scientists are currently collecting fish eggs at the Scripps pier to identify the group of fishes that are reproducing in the local marine protected area. When this is done, they will decide whether to develop a “tuned” probe array or employ alternate approaches (which will also be based on DNA barcoding principles). The ultimate goal is to be able to monitor fish reproduction more rapidly, accurately and cost effectively. Surveys of fish eggs and larvae are conducted to help estimate spawning fish biomass, from which harvesting guidelines are in part set. A better understanding of fish reproductive success, as well more information on the timing and location of spawning, would be of great value in fisheries management and in explaining natural variation in fish population sizes, as well as assessing the impacts of environmental change.