Abstract:[Background] Microalga Desmodesmus sp. QL96 was isolated from Tibet Plateau, China. We had previously found that the microalga was able to grow at both 4 °C and 25 °C, and produced 71.68% (W/W) cellular proteins which showed antioxidant activities. [Objective] Herein, an antioxidant protein in Desmodesmus sp. QL96 cells was purified and its structure was analyzed. [Methods] Purification of the antioxidant protein was performed through chromatography. The antioxidant activity of the purified protein was determined using chemiluminescence assays and in vitro cell cultures. The structure of the purified protein was then analyzed using mass spectrometery. [Results] The antioxidant protein took up 11.40% (W/W) of the dry microalgal cells. The purified protein demonstrated scavenging capacity to free radicals of OH?, DPPH, ABTS and H2O2 (over 60% scavenged). In vitro cell cultures using liver carcinoma cell HepG2 demonstrated that the Desmodesmus sp. QL96 antioxidant protein could reduce oxidative damage to the cells. The amino acid sequence of the protein determined using a mass spectrometery showed that the molecular weight of the antioxidant protein was 44.8 kD with a pI of 5.79. The homologous rate of the protein with the known proteins in NCBI was below 59%. [Conclusion] Microalga Desmodesmus sp. QL96 produces a previously uncharacterized protein which demonstrates antioxidant activity. The transcript of the protein will be analyzed to verify the genetic sequence similarity in the future, as well as its potential function and industry applications.