Marine microalgal biotoxins can accumulate in seafoods, posing significant risk to human health. These toxins include tetrodotoxin (TTX) and can cause paralytic shellfish poisoning (PSP), diarrhetic shellfish poisoning (DSP), and amnesic shellfish poisoning (ASP). With accelerating climate change, the frequency and intensity of harmful algal blooms capable of producing biotoxins have increased. In South Korea, the Ministry of Food and Drug Safety (MFDS) regulates traditional toxins, including TTX and toxins causing PSP, DSP, and ASP. In contrast, the U.S. Food and Drug Administration (FDA) and European Food Safety Authority (EFSA) have established regulatory standards for a broader spectrum of marine biotoxins, including yessotoxins (YTXs), brevetoxins (BTXs), azaspiracids (AZAs), and ciguatoxins (CTXs), to ensure seafood safety. To effectively address this global concern, the MFDS launched an R&D project entitled "Establishment of the Safety Management System for Marine Biotoxins" (2020–2024). This project focused on enhancing analytical methods to detect unregulated toxins, assessing contamination levels, and developing rapid detection techniques. The project proposal emphasizes the need to establish a comprehensive monitoring system to mitigate future risks, particularly as climate change expands the range of toxic marine species. This project aims to advance our understanding of marine biotoxin contamination and strengthen seafood safety measures in South Korea by aligning them with international standards. This special issue compiles knowledge accumulated and technical advancements related to marine biotoxins, stemming from the outcomes of this project. It includes 12 papers describing analyses of various regulated and unregulated marine biotoxins, the current prevalence of seafood contamination, toxicity assessments, rapid analytical methods, and the state of safety management.