The paper proposes a new method to automatically extract all fuzzy parameters of a Fuzzy Logic Controller (FLC) in order to control nonlinear industrial processes. The main objective of this paper is the extraction of a FLC from data extracted from a given process while it is being manually controlled. The learning of the FLC is performed by a hierarchical genetic algorithm (HGA), from a set of process-controlled input/output data. The algorithm is composed by a five level structure, being the first level responsible for the selection of an adequate set of input variables. The second level considers the encoding of the membership functions. The individual rules are defined on the third level. The set of rules are obtained on the fourth level, and finally, the fifth level selects the elements of the previous levels, as well as, the t-norm operator, inference engine and defuzzifier methods which constitute the FLC. To optimize the proposed method, the HGA’s initial populations are obtained by an initialization algorithm. This algorithm has the main goal of providing a good initial solution for membership functions and rule based populations, enhancing the GA’s tuning. Moreover, the HGA is applied to control the dissolved oxygen in an activated sludge reactor within a wastewater treatment plant. The results are presented, showing that the proposed method extracted all the parameters of the fuzzy controller, successfully controlling a nonlinear plant.