Mild, simple and efficient recovery methods are required to obtain high-value microalgae proteins. As a promising extraction method, an Aqueous two phase system (ATPS) was used to partition proteins from crude microalgae extracts obtained from two green microalgae of industrial interest: Neochlons oleoabundans and Tetraselmis suecica. Furthermore, the Non-Random Two Liquids model (NRTL) was applied to describe both the phase diagram and the partition coefficient of total protein. It was observed that total protein preferentially concentrates in the top phase. Additionally, no significant effect on partition or extraction efficiency was noted at different tie lines. Experimental data indicate that proteins and sugars are selectively fractionated in top and bottom phases respectively. The model provided a good representation of the experimental data for the liquid-liquid equilibrium. Moreover, the model also led to a good representation of the partitioning data for two reference proteins, Rubisco and Bovine Serum Albumin (BSA), as well as for total protein from crude microalgae extracts.