A tissue marking system for use in marking a tissue sample comprises an ink-based applicator device and at least one tissue marking clip. The ink-based applicator device includes a container, a first number of ink reservoirs at least partially defined by the container, wherein each reservoir contains ink of a different color, a second number of applicators, wherein each applicator is configured to absorb a quantity of ink for application to the tissue sample, and a cover coupled to and cooperating with the container to fully enclose each of the first number of ink reservoirs. The at least one tissue marking clip includes an actuator portion movable between an actuated position and a non-actuated position, and a jaw portion coupled to the actuator portion and movable between an open position and a closed position in response to movement of the actuator portion between the actuated and non-actuated positions.