The nitrification inhibitors (NIs) 3,4-dimethylpyrazole (DMPP) and dicyandiamide (DCD) can effectively reduce N2O emissions; however, which species are targeted and the effect of these NIs on the microbial nitrifier community is still unclear. Here we identified the ammonia oxidizing bacteria (AOB) species linked to N2O emissions and evaluated the effects of urea and urea with DCD and DMPP on the nitrifying community in a 258-day field experiment under sugarcane. Using an amoA AOB amplicon sequencing approach and mining a previous dataset of 16S rRNA sequences, we characterized the most likely N2O-producing AOB as a Nitrosospira spp. and identified Nitrosospira (AOB), Nitrososphaera (archaeal ammonia oxidizer) and Nitrospira (nitrite-oxidizer) as the most abundant, present nitrifiers. The fertilizer treatments had no effect on the alpha and beta diversities of the AOB communities. Interestingly, we found three clusters of co-varying variables with nitrifier operational taxonomic units (OTUs): the N2O-producing AOB Nitrosospira with N2O, NO3-, NH4+, water-filled pore space (WFPS) and pH; AOA Nitrososphaera with NO3-, NH4+ and pH; and AOA Nitrososphaera and NOB Nitrospira with NH4+, which suggests different drivers. These results support the co-occurrence of non-N2O-producing Nitrososphaera and Nitrospira in the unfertilized soils and the promotion of N2O-producing Nitrosospira under urea fertilization. Further, we suggest that DMPP is a more effective NI than DCD in tropical soil under sugarcane.