Toxins produced in biological organisms are poisons that have evolved over time in animals/plants and microbes. They are toxic to predating organisms including humans. Biotoxins give adaptive advantage to the producing organisms against predators and to combat altering climatic conditions. Recently, due to anthropogenic activities and warming of Oceans, Eutrophication alterations in pH of waters have increased the biotoxins produced in the organisms. Additionally, biotoxins can synergistically act on contaminants of emerging concern to attenuate the toxic effect on organism at ecosystem level in addition to affecting human health. Several classes of biotoxins are present and the identification of new compounds is ongoing. Over the preceding five decades, much research has gone into investigating their mode of action, how they contribute to pathogenicity, and developing antidotes that negate their influence. Further, advances in detection methods including chromatography, mass spectrometry, vibrational spectroscopy, nanotechnology have led to detect novel toxins and their mode of actions. From the regulatory perspective, there are also new demands set by global regulators like Food and Drug Administration, European Union, Therapeutic Goods Administration, and Ministry of Health and Labour Welfare, and the detection methods/production needs standardization from the industries. These are vital for food safety, bioterrorism vigilance, and environmental protection. DNA affecting property of the toxins can have therapeutic potential. Interestingly, several research groups have concentrated on the therapeutic potential of biotoxins which can be used to impede vital biological functions and/or damage the integrity of their target cells. A large-scale production of biotoxins is explored using synthetic biology and biotechnological approaches. The therapeutic potential of not only biotoxins but their conjugates with aptamers, antibodies, affibodies, and nanobodies is thrust area of research. The conjugates are characterized efficiently using physical and chemical properties in the laboratories. The mechanism of action of biotoxins and their conjugates is studied using Omic approaches such as transcriptomics, proteomics, and metabolomics in preclinical evaluations for several diseases including eye diseases. The chapter focuses on emergent biotoxins and their conjugates as potential drugs in the preclinical and clinical evaluations.