This study examines the impact of the cold tongue (CT) El Niño and the warm pool (WP) El Niño on tropical cyclone (TC) genesis over the South China Sea (SCS) from 1965 to 2010. During Sept–Oct–Nov (SON), the TC genesis exhibits clear interannual variability. SON TC genesis is significantly related with the WP Niño index, but not with the CT Niño index. It is found that in the past two decades the SCS TC genesis varies coherently with the WP Niño index on a timescale of approximately 4 years, which is in accordance with the recent increase in WP El Niño events. The distinctly different atmospheric teleconnection patterns related to the CT and WP El Niño over the SCS are responsible for these relationships. CT El Niño can induce anticyclone anomalies over the SCS and the western tropical Pacific WP. However, WP El Niño can result in dipolar patterns with anticyclone anomalies over the SCS and cyclone anomalies over the western tropical Pacific WP at low- and mid-level. These WP El Niño-related large-scale circulation anomalies enlarge the low-level northerlies over the SCS. This in turn enhances the vertical wind shear and thus suppresses TC genesis over the SCS.