Fucoidan is a water soluble sulphated polysaccharide, it is usually extracted from marine organisms. Increasing research is focusing on fucoidan and its bioactivities and health benefits. Undaria pinnatifida is regarded as an unwanted organism in New Zealand’s ocean environment, because the strong invasion and proliferation ability. This research is to extract fucoidan from different treatment and storage conditions from U. pinnatifida samples, with the aim of turning this unwanted organism into commercial profit. This study was designed to examine three main hypotheses around the impacts of processing and storage on the yield and composition of fucoidan from Undaira pinnatifida. First, potential differences if the seaweed was processed immediately as opposed to left for 24 hours. This mimics the potential for harvested seaweed to be left on a boat or wharf overnight following harvest. Second, to see if the fucoidan differs when the seaweed is processed fresh as opposed to freeze dried. This is important as drying the seaweed would add considerable cost to the processing. Finally, the difference between fucoidan extracted immediately following harvest was compared with the fuciodan from seaweed that was stored frozen for three months. This is an important comparison from an industrial point of view as the seaweed is an annual plant that can only be harvested for a few months of the year, so storing to set up a commercial scale extraction factory, it might be necessary to store the seaweed for some time before extract of the fucoidan. For each of these treatments fucoidan was extracted, passed through a range of molecular filters (<3 kDa, 3-10kDa, 10-30kDa, 30-50kDa, 50-100kDa and >100kDa) and each of these fractions were collected separately and further tested for: fucose content, sulphate content, protein content, uronic acid content and antioxidant capability. There was no significant effect of any of the treatments on total fucoidan yield, so it appears that in terms of total crude fucoidan, one can leave the seaweed for up to 24 hours before processing, can extract the fucoidan from fresh seaweed (without drying), and can store it for up to 3 months in a freezer, without a large difference in the amount of fucoidan recovered using the extraction method from this study. Fucoidan quality however, did differ in some parameters and not in others. There was no difference between the treatments in terms of the distribution of molecular weight fractions, but there were significant differences in the distribution of these molecular fractions overall, with the majority (56.03% ± 4.02SD) being over 100kDa across all treatments and a considerable proportion (37.48% ± 4.22SD) being under 3kDa. In terms of the composition of the fucoidan fractions, there were no significant differences between the three treatments tested, except more protein was found in the samples that were stored for three months. For fucose, sulphate, uronic acid and protein, there were significant differences in amount of these components in the various molecular size fractions. The 50-100 and over 100kDa fractions had the most fucose (20.29% ± 3.06SD and 20.66% ± 2.60SD respectively) and sulphate (21.91% ± 8.29SD and 21.33% ± 3.80 respectively), but little uronic acid (5.95% ± 3.40 and 7.86% ± 3.55 respectively. Protein was above 5% in all fractions except the less than 3kDa fraction. The antioxidant properties of the fucoidan fractions were high and comparable to previous studies. There was evidence that the antioxidant activity was highest in samples stored for 24 hours (as opposed to those processed within 6 hours), and lower in freeze dried vs non-freeze dried and lower in samples stored for 3 months vs samples processed right away. There was an interaction between the freeze drying and the molecular size, with the 50-100 and >100 kDa treatments within the freeze dried treatments exhibiting lower antioxidant activity. Overall this shows that the higher than 50 kDa fractions contain the most fucoidan, this fucoidan has a large protein fraction and havs the greatest antioxidant activity if it is left for processing for 24 hours, not freeze dried and not stored frozen for 3 months. Given these results, to maximise fucoidan yield and bioactivity, the seaweed should be processed around one day after collection, and the fucoidan can be extracted without first drying the seaweed.