Here, we report a genome sequence of
Afipia carboxidovorans
strain SH125 isolated from an anammox reactor. This facultative anaerobic strain possesses the clade I-type nitrous oxide (N
2
O) reductase gene, devoid of nitrite- and nitric oxide reductase genes. Deciphering the genome will help explore N
2
O reducers instrumental in N
2
O mitigation.