The physicochemical properties and antioxidant activities of two fucosylated chondroitin sulfate (ACP and HOP) isolated from sea cucumber Acaudina molpadioidea and Holothuria nobilis respectively were detected in this study. Their SEM and AFM images, conformation based on circular dichroism spectroscopy, specific optical rotation, intrinsic viscosity, and antioxidant activities were first determined. The SEM and AFM images demonstrated differences in the three-dimensional morphological features of the two polysaccharides. The CD results revealed the conformation variation of the two polysaccharides after thermal, acid and alkali treatments. The specific rotations of ACP and HOP were -46 degrees and -22 degrees respectively, and the intrinsic viscosity of ACP and HOP was 145.52 ml/g and 7.30 ml/g respectively. The antioxidant assay showed that ACP and HOP both exhibited moderate antioxidant activities against DPPH, hydroxyl, and superoxide radicals in a dose-dependent manner. Our study provides basic data for understanding the antioxidant activities of animals and exploring potential antioxidant from sea cucumber. The findings in this study also provide the basis on researching the relationship between antioxidant activities and physicochemical properties of FucCS. (C) 2016 Elsevier Ltd. All rights reserved.