Studies of ichthyoplankton in Neotropical environments have become increasingly relevant for environmental inventories and monitoring programs designed to evaluate anthropogenic impacts on ichthyofauna, especially potamodromous fish. These studies have made advancements including progress in improving techniques of data collection and processing. However, challenges remain in the taxonomic identification of ichthyoplankton organisms, especially eggs. Identification initiatives have been hindered by the paucity of literature and scientific collections, as well as the morphological similarity among species. As a result, few species have been identified during this period of development. Under these circumstances, the information provided by egg sampling has been underutilized, and quantification of eggs is commonplace, even in regions where they are predominant in the ichthyoplankton. Limited data on fish species at the egg/larvae stages make it impossible to determine spawning periods and sites of a specific taxonomic group. To address these challenges, we have developed a live ichthyoplankton identification technique which enables the identification of eggs collected from fish, especially migratory species, using a novel method of processing ichthyoplankton. In addition, we cite case studies highlighting the application of this technique. Data from these studies can inform management and monitoring programs in such areas as identification of spawning areas, formation of breeding stock, restocking of native fish, and improvement of scientific collections of ichthyoplankton. Thus, we believe that this new taxonomic technique for identifying live ichthyoplankton represents a paradigm shift in fish monitoring, management, and conservation, as well as ecological management.