With thousands of sequenced 16 S rRNA genes available, and advancements in oligonucleotide microarray technology, the detection of microorganisms in microbial communities consisting of hundreds of species may be possible. The existing algorithms developed for sequence-specific probe design are not suitable for applications in large-scale bacteria detection due to the lack of coverage, flexibility and efficiency. Many other strategies developed for group-specific probe design focus on how to find a unique group-specific probe that can specifically detect all target sequences of a group. Unique group-specific probe for each group can not always be found. Hence, it is necessary to design non-unique probes. Each probe can specifically detect target sequences of a different subgroup. Combination of multiple probes can achieve higher coverage. However, it is a time-consuming task to evaluate all possible combinations. A feasible algorithm using relative entropy and genetic algorithm (GA) to design group-specific non-unique probes was presented.