Security ontology can be used to build a shared knowledge model for an application domain to overcome the data heterogeneity issue, but it suffers from its own heterogeneity issue. Finding identical entities in two ontologies, i.e., ontology alignment, is a solution. It is important to select an effective similarity measure (SM) to distinguish heterogeneous entities. However, due to the complex semantic relationships among concepts, no SM is ensured to be effective in all alignment tasks. The aggregation of SMs so that their advantages and disadvantages complement each other directly affects the quality of alignments. In this work, we formally define this problem, discuss its challenges, and present a problem-specific genetic algorithm (GA) to effectively address it. We experimentally test our approach on bibliographic tracks provided by OAEI and five pairs of security ontologies. The results show that GA can effectively address different heterogeneous ontology-alignment tasks and determine high-quality security ontology alignments.