Fuels produced from microalgae are a promising alternative to fuels from fossil resources. Algae biomass can be transformed by means of hydrothermal liquefaction (HTL) into biocrudes, which need upgrading by hydrotreatment to meet transportation fuel requirements. This study presents analyses of HTL biocrude catalytically hydrogenated in a batch reactor at temperatures between 360 and 400 degrees C and residence times between 2.5 and 10.2 h. Selected samples were analyzed using Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). The goal of the analysis was to characterize higher-molecular-weight components in the biocrude. Electrospray ionization in positive and negative ion modes was successfully applied to ionize heteroatomic compounds and, depending on the ionization mode and sample, molecular formulas between 200 and 1200 u were observed. Several molecular formulas were identified containing oxygen, nitrogen, sulfur, and phosphorous and with carbon numbers (n(C)) between 10 and 60. The results show that the number of observable heteroatomic molecular formulas increases for samples representing intermediate hydrogenation conditions compared to the crude, and decreases at higher temperatures and times. Nitrogen compounds of type CcHhNn with n >= 2 are more easily removed from the samples than those with n = 1. Also, the fate of oxygen compounds can be tracked upon hydrogenation, revealing that phenols are effectively removed, but aliphatic and monounsaturated carboxylic acids are still present in samples representing the greatest hydrogenation progress. The analysis allows the decrease of heteroatomic compounds to be tracked and facilitates the selection of optimum parameters for the hydrogenation of HTL biocrudes from algae.