Fish is a vital entity of aquatic biodiversity contributing immensely to ecosystem functions and ecological services including nutritional and economical support to mankind. Currently, fishes have been exposed to biotoxins such as ciguatoxins, microcystins, okadaic acid, etc., produced by harmful algal blooms (HABs) occurring in various degraded aquatic systems. These toxins when ingested by finfishes and shellfishes get accumulated at hazardous levels in their tissues which eventually penetrate into the food chain, affecting a wide spectrum of species. Biotoxins are quite persistent in the environment because of their high stability and low degradability. It is predicted that with climate change, the occurrence of HABs and production of biotoxins will increase which demands monitoring of such outbreaks and assessment of associated ecotoxicological risk. Hence, fast detection, identification, and quantification of biotoxins affecting finfish and shellfish are of utmost importance. Biosensors have proved to be rapid, cost-effective, specific, sensitive, and real-time devices for detecting biotoxins as compared to the classical Mouse Based Assay (MBA), chromatographic, and spectroscopic methods. This chapter aims to elucidate the application of biosensors in detecting biotoxins affecting finfish and shellfish, their limitations and future prospects as a durable sensing device to tackle and mitigate the environmental, health, and economic implications, globally.