In this study, a techno-economic analysis is performed to analyze the effect of the choice of microalgal species on the economics of microalgae-based lipid production. Three microalgal species (Chlorella vulgaris, Tetraselmis suecica, and Nannochloropsis sp.) are selected given their disparate cell characteristics and high promise as feedstocks for commercial scale microalgae-based lipid production. In the economic analysis, significantly different total production costs are obtained for the three species ($6.5/kg(lipid), $7.0/kg(lipid), and $8.3/kg(lipid) for Chlorella vulgaris, Tetraselmis suecica, and Nannochloropsis sp., respectively), and the percentage of each processing stage contributing to the total cost also turned out to be quite different depending on the species. On the basis of the economic analysis, a sensitivity analysis is performed to analyze the effect of different cell characteristics on the overall economics, and to identify the most influential characteristic. The further scenario-based analysis shows that the economic results, as well as the relative standings of the species, change significantly when processing technologies are changed, pointing to the need to optimize the processing pathway individually for each species for a fair evaluation.