Metabolic flux analysis (MFA) is one of the pillars of metabolic engineering. Over the past three decades, it has been widely used to quantify intracellular metabolic fluxes in both native (wild type) and engineered biological systems. Through MFA, changes in metabolic pathway fluxes are quantified that result from genetic and/or environmental interventions. This information, in turn, provides insights into the regulation of metabolic pathways and may suggest new targets for further metabolic engineering of the strains. In this mini-review, we discuss and classify the various methods of MFA that have been developed, which include stoichiometric MFA, (13)C metabolic flux analysis, isotopic non-stationary (13)C metabolic flux analysis, dynamic metabolic flux analysis, and (13)C dynamic metabolic flux analysis. For each method, we discuss key advantages and limitations and conclude by highlighting important recent advances in flux analysis approaches.