The anaerobic ammonium-oxidizing (anammox) and nitrite-dependent anaerobic methane-oxidizing (n-damo) bacteria in a paddy soil core (0–100 cm) were investigated with newly designed primers targeting the hydrazine synthase β-subunit (hzsB) of anammox bacteria and the recently published primers targeting the pmoA and 16S rRNA genes of n-damo bacteria. The hzsB gene was identified as a proper biomarker to explore the anammox bacterial biodiversity and abundance in soil. The anammox bacteria were present throughout the soil core with the highest abundance of 2.7 × 106 hzsB copies g−1 dry soil at 40–50 cm and were not detectable below 70 cm. Sequences related to at least three species of known anammox bacteria, ‘Brocadia anammoxidans’, ‘Brocadia fulgida’, and ‘Jettenia asiatica’ were detected. By combining the analysis of pmoA and 16S rRNA genes, the n-damo bacteria were observed to be present in 30–70 cm with abundance from 6.5 × 103 (60–70 cm) to 7.5 × 104 (30–40 cm) copies g−1 dry soil. The pmoA sequences retrieved from different depths closely related to each other and formed a unique clade. Our results showed that anammox and n-damo bacteria co-occurred in the paddy soil. Both of them were abundant in deep layers (30–60 cm) and the community structures changed along depths in the soil core.