Microcystins (MCs) are cyclic heptapeptidic toxins produced by many cyanobacteria. Microcystins can be accumulated in various matrices in two forms: a free cellular fraction and a covalently protein-bound form. To detect and quantify the concentration of microcystins, a panel of techniques on various matrices (water, sediments, and animal tissues) is available. The analysis of MCs can concern the free or the total (free plus covalently bound) fractions. Free-form analyses of MCs are the most common and easiest to detect, whereas total-form analyses are much less frequent and more complex to achieve. The objective of this review is to summarize the different methods of extraction and analysis that have been developed for total forms. Four extraction methods were identified: MMPB (2-methyl-3-methoxy-4-phenylbutyric acid) method, deconjugation at basic pH, ozonolysis, and laser irradiation desorption. The study of the bibliography on the methods of extraction and analysis of the total forms of MCs showed that the reference method for the subject remains the MMPB method even if alternative methods and, in particular, deconjugation at basic pH, showed results encouraging the continuation of the methodological development on different matrices and on naturally-contaminated samples.