A recursive algorithm for the two-stage empirical frequency-domain optimal parameter (EFOP) estimation method was proposed. The EFOP method was a novel system identification method for Black-box models that combines time-domain estimation and frequency-domain estimation. It has improved anti-disturbance performance, and could precisely identify models with fewer sample numbers. The two- stage EFOP method based on the boot-strap technique was generally suitable for Black-box models, but it was an iterative method and takes too much computation work so that it did not work well online. A recursive algorithm was proposed for dis- turbed stochastic systems. Some simulation examples are included to demonstrate the validity of the new method.