Marine organisms have been increasingly regarded as an excellent source of bioactive molecules for human health. As part of an on-going study to elucidate the chemical composition and biological activity of this organism, we report here the lipidomic profile of this organism and screening for anticancer activity. Two classes of biologically active metabolites were identified and quantified by a GC-MS optimized method for screening several classes of metabolites in a single run. Free fatty acids and sterols were found, including ergosterol, β-sitosterol and cholesterol derivatives, some of which are reported in this species for the first time. Distinct assays were performed to screen extract’s effect on viability, membrane integrity and density of three human cancer cell lines: human oestrogen receptor-positive (ER+) breast cancer (MCF-7), human neuroblastoma (SH-SY5Y) and human colon cancer (Caco-2). Differential activity towards the three cancer cell lines was found, SH-SY5Y cell line being the most susceptible. No activity was found for Caco-2 cell line. Non-cancer cell lines (human dermal fibroblasts and human foreskin fibroblasts) were also tested and revealed to be less susceptible. This work establishes M. glacialis as a potential source of bioactive molecules for further studies.