The global and Amazon climate change, mainly in rainfall, due to the El Nino and La Nina phenomena. The objective of this study was to analyze the relative frequency (RF) of rainfall, in different periods of the day, during occurrences of El Nino, La Nina events and neutrality condition. The research was carried out in the Southern mesoregion of the state of Amazonas (Apui, Boca do Acre, Labrea, Manicore and Humaita). Data were analyzed by the Spiegel ' s method. The rainfall data were obtained from the Global Land Data Assimilation database from January 1st, 2000 to December 31st, 2018. Data were made available every three hours and integrated into six hours. RF of rainfall was higher in the afternoon in La Nina, Neutro and El Nino years in all municipalities. The RF in La Nina year was higher than during El Nino. The RF during the Neutral year was higher than during El Nino in Apui and Boca do Acre, and had no difference in Labrea, Manicore and Humaita. The rainfall in the southern Amazon mesoregion was more frequent during the afternoon.