Microalgae show great potential for use as novel ingredients in food products, as they are rich in several nutritional and health-beneficial components. However, addition of total microalgal biomass might alter the structural properties of the food system. Therefore, information is required about their rheological characteristics towards selection of microalgae species for specific food products. This study comprises the rheological characterization of seven commercially available microalgae species in aqueous suspensions, before and after mechanical and thermal processing. Substantial differences in rheological properties were observed between the investigated microalgal suspensions. Among the untreated suspensions, Porphyridium cruentum, Chlorella vulgaris and Odontella aurita showed the largest structural properties and could be described as weak gels. All suspensions showed shear-thinning flow behavior at the examined concentration of 8% w/w, except for Nannochloropsis species. Shear-thinning behavior was also observed for the separated serum phase of P. cruentum, which might be attributed to the presence of sulfated exopolysaccharides. During processing, rheological properties were significantly altered. High pressure homogenization was used as a mechanical treatment, followed by a pasteurization or sterilization process. Whereas suspensions of Arthrospira platensis and C. vulgaris showed an increased storage modulus and viscosity after processing, the opposite was observed for P. cruentum and O. aurita. No clear effect of processing was observed for suspensions of Nannochloropsis sp., Schizochytrium sp. and Phaeodactylum tricornutum. Investigation of the microstructure revealed differences in degree of cell disruption by high pressure homogenization, with Nannochloropsis sp. being the most resistant. Subsequent thermal processing resulted in aggregation of released cell material and/or intact cells. In conclusion, the obtained results provide the scientific knowledge base for the selection of microalgae species towards food applications. Whereas some microalgae species hardly affect the structural properties of the food product, other microalgae species show large potential for use as a structuring agent in food applications.