Natural source of coagulant is certainly being considered in addressing the disadvantages associated with the use of inorganic coagulants. Annona muricata is hypothesized to be new material as natural coagulant aid in coagulation-flocculation process. On the other hand, due to the high lipids content in microalgae, namely, Chlorella vulgaris is used in producing renewable energy, i.e. biodiesel. Coagulation-flocculation is an effective method in microalgae harvesting. Thus, in this study, a novel natural coagulant aid extracted from fruit waste in algae harvesting. It is aimed to (1) to extract natural coagulant aid (hereafter is known as biopolymer) extracted from Annona muricata seeds in algae harvesting, and (2) to evaluate the operational conditions of coagulation-flocculation process by utilizing the biopolymer. As a result, it is observed that acid extraction and extraction through sodium chloride does not show any yield. On the other hand, the harvesting efficiency showed positive response as coagulant aid at 20 mg/L. © The Authors, published by EDP Sciences, 2018.