Microalgae are a promising feedstock for biofuels production and other applications; however, the high costs associated with algal biomass separation hinder its large scale development. The application of an effective and inexpensive harvesting method is essential for achieving a viable process. For this reason, the mechanism of pH induced flocculation for Skeletonema Costatum and Chaetoceros Gracilis microalgae has been evaluated in this research. Acid pH values (2–6) and basic pH values (8–12) have been tested for both species. Almost a total algal biomass recovery has been reached for the highest pH values (11, 11.5 and 12); while a maximum biomass recovery, around 60%, has been achieved for acid pH values, for both species. Salinity effect on harvesting efficiency has also been tested. Minor effects have been detected for long time intervals. After biomass separation, oil extraction was conducted using two different techniques: ultrasound and Soxhlet. Similar yields were obtained with two techniques. In addition, chromatographic analysis of algal oil showed that all fatty acids present are saturated. Thus, the obtained results showed that pH induced flocculation could be a promising harvesting method. The two studied algal species appear to be a potential and suitable raw material for obtaining lipids.