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Objective: To determine the significance of temperature, rainfall and humidity in the seasonal abundance of Anopheles stephensi in south Iran. Methods: Data on the monthly abundance of Anopheles stephensi larvae and adults were gathered from earlier studies conducted between 2002 and 2019 in malaria prone areas of southeast Iran. Climatic data for the studied counties were obtained from climatology stations. Generalized estimating equations method was used for cluster correlation of data for each study site in different years. Results: A significant relationship was found between monthly density of adult and larvae of Anopheles stephensi and precipitation, max temperature and mean temperature, both with simple and multiple generalized estimating equations analysis (P<0.05). But when analysis was done with one month lag, only relationship between monthly density of adults and larvae of Anopheles stephensi and max temperature was significant (P<0.05). Conclusions: This study provides a basis for developing multivariate time series models, which can be used to develop improved appropriate epidemic prediction systems for these areas. Long-term entomological study in the studied sites by expert teams is recommended to compare the abundance of malaria vectors in the different areas and their association with climatic variables.