Parameter identification is an important research topic with a variety of applications in industrial and environmental problems. Usually, a functional has to be minimized in conjunction with parameter identification; thus, there is a certain similarity between the parameter identification and optimization. A number of rigorous and efficient algorithms for optimization problems were developed in recent decades for the case of a convex functional. In the case of a non-convex functional, the metaheuristic algorithms dominate. This paper discusses an optimization method called modified bee colony algorithm (MBC), which is a modification of the standard bees algorithm (SBA). The SBA is inspired by a particular intelligent behavior of honeybee swarms. The algorithm is adapted for the parameter identification of reaction-dominated pore-scale transport when a non-convex functional has to be minimized. The algorithm is first checked by solving a few benchmark problems, namely finding the minima for Shekel, Rosenbrock, Himmelblau and Rastrigin functions. A statistical analysis was carried out to compare the performance of MBC with the SBA and the artificial bee colony (ABC) algorithm. Next, MBC is applied to identify the three parameters in the Langmuir isotherm, which is used to describe the considered reaction. Here, 2D periodic porous media were considered. The simulation results show that the MBC algorithm can be successfully used for identifying admissible sets for the reaction parameters in reaction-dominated transport characterized by low Pecklet and high Damkholer numbers. Finite element approximation in space and implicit time discretization are exploited to solve the direct problem.