Ammonia monooxygenase subunit A (amoA) gene have been widely used for investigating phylogenetic diversity and spatial distribution of ammonia-oxidizing archaeal (AOA) and bacterial (AOB) populations, which make a great contribution to the nitrogen cycle in diverse environments on the earth. Here, using a probe capture hybridization technique, we developed a novel amoA gene enrichment sequencing method from metagenomes and metatranscriptomes.