FPGAs are becoming increasingly attractive – thanks to the improvement of their capacities and their performances. Today, FPGAs represent an efficient design solution for numerous systems. Moreover, since FPGAs are important for electronic industry, it becomes necessary to improve their security, particularly for SRAM FPGAs, since they are more vulnerable than other FPGA technologies. This paper proposes a solution to improve the security of SRAM FPGAs through flexible bitstream encryption. This proposition is distinct from other works because it uses the latest capabilities of SRAM FPGAs like partial dynamic reconfiguration and self-reconfiguration. It does not need an external battery to store the secret key. It opens a new way of application partitioning oriented by the security policy.