There has been a rising concern regarding the harmful impact of biotoxins, source of origin, and the determination of the specific type of toxin. With numerous reports on their extensive spread, biotoxins pose a critical challenge to figure out their parent groups, metabolites, and concentration. In that aspect, liquid chromatography‐mass spectrometry (LC‐MS) based analysis paves the way for its accurate identification and quantification. The biotoxins are ideally categorized as phytotoxins, mycotoxins, shellfish‐toxins, ciguatoxins, cyanotoxins, and bacterial toxins such as tetrodotoxins. Considering the diverse nature of biotoxins, both low‐resolution mass spectrometry (LRMS) and high‐resolution mass spectrometry (HRMS) methods have been implemented for their detection. The sample preparation strategy for complex matrix usually includes “QuEChERS” extraction or solid‐phase extraction coupled with homogenization and centrifugation. For targeted analysis of biotoxins, the LRMS consisting of a tandem mass spectrometer operating in multiple reaction monitoring mode has been widely implemented. With the help of the reference standard, most of the toxins were accurately quantified. At the same time, the suspect screening and nontarget screening approach are facilitated by the HRMS platforms during the absence of reference standards. Significant progress has also been made in sampling device employment, utilizing novel sample preparation strategies, synthesizing toxin standards, employing hybrid MS platforms, and the associated data interpretation. This critical review attempts to elucidate the progress in LC‐MS based analysis in the determination of biotoxins while pointing out major challenges and suggestions for future development.