Dicyandiamide, a routinely used commercial nitrification inhibitor (NI), inhibits ammonia oxidation catalyzed by ammonia monooxygenase (AMO). Phenylhydrazine hydrochloride has shown considerable potential for the development of next-generation NIs targeting hydroxylamine dehydrogenase (HAO). The effects of the AMO inhibitor and the HAO inhibitor on ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) present in agricultural soils have not been compared thus far. In the present study, the effects of the two inhibitors on soil nitrification and the abundance of AOA and AOB as well as their community structure were investigated in a soil microcosm using quantitative polymerase chain reaction and pyrosequencing. The net nitrification rates and the growth of AOA and AOB in this soil microcosm were inhibited by both NIs. Both NIs had limited effect on the community structure of AOB and no effect on that of AOA in this soil microcosm. The effects of phenylhydrazine hydrochloride were similar to those of dicyandiamide. These results indicated that organohydrazine-based NIs have potential for the development of next-generation NIs targeting HAO in the future.