Mechatronic systems operating in industrial environments are subject to a variety of threats because of harsh conditions. Industrial systems usually use commercial off-the shelf (COTS) equipment which are not robust and safe against hostile conditions and therefore require fault-tolerance considerations. This paper presents a novel and efficient method for online detection of control flow errors, called software-based control flow checking (SCFC). It is implemented purely in software and does not manipulate the hardware architecture of the system. Redundant instructions and signatures are embedded into the program at compile time and are utilized for control flow checking at run time. The signatures of the basic blocks are derived from the program graph. It is shown in the paper that SCFC method can increase single detection capability to 14.7% and the fault coverage to 6.12% averagely in comparison with other methods without any increase in memory and performance overheads. In the paper, besides experimental evaluations, analytical evaluations are also carried out, based on probability principles. The detection ability of each method used is thus computed. These computations verify the experimental results and show that SCFC can detect more errors than other methods suggested in literature. Considering the memory limitations in some (such as space) applications and the trend towards the requirement for faster execution of programs, we suggest a novel metric called fitness parameter which incorporates these. It is a better measure than the previously proposed ones since it considers the fault coverage, the memory overhead and the execution time (performance overhead) of each method simultaneously, as well as the detection capability.