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The extraction of lipids from microalgal cells using ultrasonic and microwave pretreatments is mechanistically evaluated based on the distribution of cell fragments, the lipid content analysis, the scanning electron microscopic (SEM) observation of ruptured microalgal cells, and the analysis of fatty acids. The results indicate that microwave pretreatment extracts lipids more rapidly and efficiently as compared to ultrasonic pretreatment. The rupture of cells in the microwave process is due to the tremendous pressure caused by the rapid heating of the moisture inside the microalgal cells, whereas in the ultrasonic process the microalgal cells are ruptured by shock waves from cavitation bubbles outside the cells. The fatty acid composition of the respective lipids extracted via the two types of pretreatment did not vary significantly from one another. These results demonstrate that the microwave process is rapid and more effective than the ultrasonic process for lipid extraction from microalgae.