Microalgae is an attractive feedstock for sustainable biodiesel production. The harvesting step of microalgae needs technology, which saves energy and time. One of the low cost strategies for addressing this problem is the use of flocculation-sedimentation process as an initial step. The aim of the present study is to evaluate the flocculation-sedimentation of selected microalgae species grown in monoculture (Nannochloropsis sp.) and mixed cultures (South Coast of Yogyakarta) using modified chitosan. The effect of flocculant dosage and sedimentation time that might affect the percentage of microalgae cell removal was investigated. Chitosan has proved to be highly effective for dewatering of the microalgae, Nannochloropsis sp. and Yogyakarta mixed cultures, with the optimum flocculation efficiency reaching over 72.09 % (25 ppm of chitosan dosage; 10 min of sedimentation time) and 87.25 % (25 ppm of chitosan dosage; 30 min of sedimentation time) of biomass removal. The characteristics of chitosan in term of high positive charge density and long chains allow the microalgae to aggregate to form flocs and settle to the bottom due to gravitational effect.