Lipophilic marine toxins (LMTs) are a group of marine toxins which in recent years have been consistently identified in the vast majority of shellfish worldwide. One of their main characteristics is having a latitudinal variability and an assimilation/retention specific for each species. LMTs consist of four important groups: okadaic acid group (OA-group), pectenotoxin group (PTX-group), azaspiracid group (AZA-group) and yessotoxin group (YTX-group). These groups have different chemical structures, which has generated an important challenge to establish analytical techniques to identify all toxic analogues from the same toxic matrix. Likewise, in the aquatic environment, shellfish represent the best bio-indicator model that allows for the establishment of levels of toxicities related to LMTs. In this chapter, the evolution for detection of LMTs from mouse bioassay (MBA), enzymatic assays (PP2a), and analytical techniques, such as liquid chromatography tandem-mass spectrometry (LC-MS/MS), are described. These analytical advances have allowed us to determine and identify the characteristic profiles of LMTs produced by marine microalgae, including the prevalence and biotransformation of LMTs in the different endemic species. It is worth mentioning that these techniques have favoured the updating of numerous sanitary standards and the definition of the most appropriate technique for the detection of LMTs in shellfish and endemic species.