An increasing number of reports have been published concerning microplastic (MP) pollution in aquatic environments. Methods used in these studies continue to be updated and lack standardization, so that an up-to-date review pertaining methods for MP research is needed. This critical review examines the analytical methods, including sampling, identification, and quantitation, for MP research. Samples are generally collected from water, sediment, and biota gastrointestinal tract. Manta nets or trawls are prevalently used in surface water sampling, while direct shoveling or box-corer grab are commonly applied in sediment sampling. Microplastics in biota are generally obtained by dissecting organisms and separating livers, gills, and guts. Density separation is frequently chosen to separate MPs from sample matrices. Chemical digestion can dissolve other organic materials and isolate MPs for further identification. Visual sorting should be combined with chemical composition analysis to better identify the polymer type. Pyrolysis or thermal decomposition gas chromatography coupled with mass spectrometry, Fourier transform infrared spectroscopy, and Raman spectroscopy are currently the main technologies for MP identification. Units prevalently used to express MP abundance in water, sediment, and biota are "particles per m3," "particles per m2," and "particles per individual," respectively. As MP abundances often varied with the methods used, we recommend that analytical protocols of MPs should better be standardized and optimized. Despite the important progress in analysis of MPs, detection technologies for identifying nano-sized plastic particles are still lacking, and therefore should be developed swiftly.