The bio-crude oil produced from hydrothermal liquefaction (HTL) of a high-protein microalgae useful for wastewater treatment, Galdieria sulphuraria, was comprehensively characterized, and compared to that of a high lipid microalgae useful for biofuel production, Nannochloropsis sauna. HTL was conducted in a batch reactor at temperatures of 310-350 degrees C and reaction times of 5-60 min. Characterization methods included high-resolution Fourier transform ion cyclotron resonance mass spectroscopy (FT-ICR MS), fatty add methyl ester (FAME) analysis by gas chromatography mass spectroscopy (GC/MS), proton nuclear magnetic resonance spectroscopy (H-1 NMR), and Fourier transform infrared spectroscopy (FT-IR). Milder reaction conditions favored bio-crude oil yield and quality for N. sauna, while more severe conditions (350 degrees C) were needed for G. sulphuraria. N. salinaderived bio-crude oil contained mainly C-14-C-18 fatty acid amides, while G. sulphuraria-derived bio-crude-oil had many N1-3O0-2 hetero-atom compounds. FT-ICR MS showed that the aromaticity of hetero-compounds in N. sauna bio-crude oil was higher due to N. sauna's higher carbohydrate content and the tendency of carbohydrate derived molecules to condense at HTL conditions. FAME-GC/MS and H-1-NMR results showed that stable fatty acid amides increased in G. suiphuraria bio-crude oil at higher temperatures as more protein-derived compounds combined with lipid-derived compounds. While N-containing and high molecular weight compounds are a concern for the upgrading of bio-crude oils obtained from high-protein algal biomass, removal of carbohydrates rather than removal of proteins as a pretreatment to HTL is recommended since carbohydrate-derived compounds are more likely to create highly aromatic hetero-compounds that are much more difficult to upgrade.