Genome assembly is a prerequisite step for analyzing next generation sequencing data and also far from being solved.Many assembly tools have been pro-posed and used extensively. Majority of them aim to as-semble sequencing reads into contigs; however, we focus on the assembly of contigs into scaffolds in this paper. This is called scaffolding, which estimates the relative or-der of the contigs as well as the size of the gaps between these contigs. Pheromone trail-based genetic algorithm (PGA) was previously proposed and had decent perfor-mance according to their paper. From our previous study, we found that family competition mechanism in genetic algorithm is able to further improve the results. Therefore, we proposed family competition pheromone genetic algo-rithm (FCPGA) and also demonstrated the improvement over PGA.