The 2nd Workshop on the Security of Industrial Control Systems and of Cyber-Physical Systems (CyberICPS 2016) will be held in Heraklion, Crete, Greece, in conjunction with ESORICS 2016, in September 2016. CyberICPS is the result of the merging of the CyberICS and WOS-CPS workshops that were held for the first time in conjunction with ESORICS 2015. Cyber-physical systems (CPS) are physical and engineered systems that interact with the physical environment, whose operations are monitored, coordinated, controlled and integrated by information and communication technologies. These systems exist everywhere around us, and range in size, complexity and criticality, from embedded systems used in smart vehicles, to SCADA systems in smart grids to control systems in water distribution systems, to smart transportation systems, to plant control systems, engineering workstations, substation equipment, programmable logic controllers (PLCs), and other Industrial Control Systems (ICS). As ICS and CPS proliferate, and increasingly interact with us and affect our life, their security becomes of paramount importance. CyberICPS intends to bring together researchers, engineers and governmental actors with an interest in the security of ICS and CPS in the context of their increasing exposure to cyber-space, by offering a forum for discussion on all issues related to their cyber security.