Calanus finmarchicus is one of the most important zooplankton species in the North Atlantic. The zooplankton is currently being harvested and industrially processed to a marine oil product for human consumption as a marine nutraceutical containing long-chain omega-3 polyunsaturated fatty acids. This oil is very rich in wax esters, a lipid class where fatty acids are esterified to long chain fatty alcohols. In this paper we describe a simple method to 1) isolate the wax esters from the other lipid classes present in the oil, 2) hydrolyze the wax esters, and 3) separate the fatty acids from the fatty alcohol, all by means of solid phase extraction. Starting with an average of 322 mg Calanus oil, we obtained 75 mg fatty alcohols and 63 mg fatty acids. Contrary to previously described techniques, our method neither oxidize the fatty alcohols to fatty acids, nor are the fatty acids methylated, allowing the native, unesterified fatty acids and fatty alcohols to be used for further studies, such as in cell culture experiments to study the metabolic effects of these specific lipid fractions rather than the intact oil or wax esters.