In this paper, a newly developed multi-agent meta-heuristic method, named Cyclical Parthenogenesis Algorithm (CPA), is incorporated into a guided modal strain energy based structural damage detection technique. A modal strain energy based index is used to guide the structural damage identification process, which is formulated as an inverse optimization problem. Generalized Flexibility Matrix (GFM) of the structure is used to define the objective function of the optimization problem. Three numerical examples are provided in order to examine the viability of the proposed method. The results indicate that the proposed method is capable of locating and quantifying structural damage using only the first few modes of the structure. The results are also compared with those of three other meta-heuristic algorithms in order to show the efficiency of CPA in solving the problem.