Simple SummaryOne of the greatest challenges to achieving a sustainable aquaculture is finding alternatives to fishmeal as a primary protein source in aquafeeds. Insects represent one of the most promising alternatives being explored and produced as replacements for this ingredient. This review addresses the use of two insect species (black soldier fly,Hermetia illucens, and yellow mealworm,Tenebrio molitor) in freshwater and marine fish diet formulations and the effect of insect meal on fish gut microbiota. Furthermore, the effects of a probiotic, namely,Lactococcus lactissubsp.lactis, are considered. The study of fish gut microbiota is very important for aquaculture practice as gut microbiota plays a significant role in nutrition metabolism, also affecting a number of other physiological functions, including fish growth and development, immune response, and pathogen resistance. Along with recent and promising results in this field, new insights and future directions on fish gut microbiota research are highlighted.AbstractAquaculture is the fastest-growing agricultural industry in the world. Fishmeal is an essential component of commercial fish diets, but its long-term sustainability is a concern. Therefore, it is important to find alternatives to fishmeal that have a similar nutritional value and, at the same time, are affordable and readily available. The search for high-quality alternatives to fishmeal and fish oil has interested researchers worldwide. Over the past 20 years, different insect meals have been studied as a potential alternate source of fishmeal in aquafeeds. On the other hand, probiotics—live microbial strains—are being used as dietary supplements and showing beneficial effects on fish growth and health status. Fish gut microbiota plays a significant role in nutrition metabolism, which affects a number of other physiological functions, including fish growth and development, immune regulation, and pathogen resistance. One of the key reasons for studying fish gut microbiota is the possibility to modify microbial communities that inhabit the intestine to benefit host growth and health. The development of DNA sequencing technologies and advanced bioinformatics tools has made metagenomic analysis a feasible method for researching gut microbes. In this review, we analyze and summarize the current knowledge provided by studies of our research group on using insect meal and probiotic supplements in aquafeed formulations and their effects on different fish gut microbiota. We also highlight future research directions to make insect meals a key source of proteins for sustainable aquaculture and explore the challenges associated with the use of probiotics. Insect meals and probiotics will undoubtedly have a positive effect on the long-term sustainability and profitability of aquaculture.