Microalgae strain selection is a vital step in the production of biodiesel from microalgae. In this study, Multi-Criteria Decision Analysis (MCDA) methodologies are adopted to resolve this problem. The aim of this study is to identify the best microalgae strain for viable biodiesel production. The microalgae strains considered here are Heynigia sp., Scenedesmus sp., Niracticinium sp., Chlorella vulgaris, Chlorella sorokiniana and Auxenochlorella protothecoides. The five MCDA methods used to evaluate different strains of microalgae are Analytic Hierarchy Process (AHP), Weighted Sum Method (WSM), Weighted Product Method (WPM), Discrete Compromise Programming (DCP) and Technique for the Order of Preference to the Ideal Solution (TOPSIS). Pairwise comparison matrices are used to determine the weights of the evaluation criteria and it is observed that the most important evaluation criteria are lipid content and growth rate. From the results, Scenedesmus sp. is selected as the best microalgae strain among the six alternatives due to its high lipid content and relatively fast growth rate. The AHP is the most comprehensive of the five MCDA methods because it considers the importance of each criterion and inconsistencies in the rankings are verified. The implementation of the MCDA methods and the results from this study provide an idea of how MCDA can be applied in microalgae strain selection. (C) 2015 Elsevier Ltd. All rights reserved.