Highly branched isoprenoid lipid (HBI) biomarkers have been reported in a wide range of Arctic animals spanning all trophic levels. The HBI biomarker-based ‘H-Print’ has been used to estimate the relative contributions of sea ice- and phytoplankton-derived primary production utilised by Arctic animals. The resulting data are providing insight into the future impact of climate change-associated sea ice decline on ecosystems. Given the range of methods available to preserve biological tissues between sampling and analysis, it was considered important to test the suitability of these methods for storage prior to the analysis of HBI lipids. In the laboratory, Artemia sp. were fed diatoms containing HBIs of known proportion. These were then harvested and stored wet- and dry-frozen and in ethanol and 4% formalin. After 6 months, Artemia sp. H-Prints stored in ethanol were significantly different from the control, whereas H-Prints from all other methods were not significantly different from the control. Dry-frozen Artemia sp. H-Prints bared the closest similarity to the control, representing the best method tested for tissue preservation prior to analysis of HBIs. This study will contribute to improving the robustness of HBI-based H-Print analyses in rapidly changing Arctic ecosystems.