Kinesin and muscle myosin are considered as physical bio-nanoagents able to sense their cells through their sensors, make decision internally, and perform actions through their actuators. This paper has investigated and compared the flexible (reactive, pro-active, and interactive) autonomous behaviors of kinesin and muscle myosin bio-nanorobots. Using an automata algorithm, the agent-based deterministic finite automaton models of the internal decision making processes of the bio-nanorobots (as their reactive and pro-active capabilities) were converted to their respective computational regular languages (as their interactive capabilities). The resulted computational languages could represent the flexible autonomous behaviors of the bio-nanorobots. The proposed regular languages also reflected the degree of the autonomy and intelligence of internal decision-making processes of the bio-nanorobots in response to their environments. The comparison of flexible autonomous behaviors of kinesin and muscle myosin bio-nanorobots indicated that both bio-nanorobots employed regular languages to interact with their environments through two sensors and one actuator. Moreover, the results showed that kinesin bio-nanorobot used a more complex regular language to interact with its environment compared with muscle myosin bio-nanorobot. Therefore, our results have revealed that the flexible autonomous behavior of kinesin bio-nanorobot was more complicated than the flexible autonomous behavior of muscle myosin bio-nanorobot.