Entomological indicators of onchocerciasis transmission and the effect of climatic variables on the vector population dynamics were investigated in two first-line villages after more than two decades of mass drug administration with ivermectin. Female blackflies were collected in two villages (Bayomen and Biatsota) using human landing method for a period of 12 months. Blackflies were dissected and entomological indices were computed. Monthly temperature, precipitation, and humidity were collected and the Spearman correlation rank test was used to assess the relationship between biting rates and climatic variables. The highest biting rates (62,280 bites/human/month in Bayomen and 42,090 bites/human/month in Biatsota) were recorded during the long rainy season (November). The Onchocerca volvulus transmission was greater during the long dry season in both villages, with a peak at the beginning of the long dry season in Biatsota (100 infective larvae/human/month), and at the middle of the long dry season in Bayomen (92 infective larvae/human/month). No correlation was found between biting rates and selected climatic variables in the two villages. This study revealed that onchocerciasis transmission is ongoing in the study area despite almost 25 years of Community-Directed Treatment with Ivermectin. In accordance with WHO recommendations, vector control should be used in combination with mass drug administration to accelerate transmission interruption of onchocerciasis. To be optimal, this vector control should be implemented during the long dry season (November to March) when water volumes are low and transmission potentials are high.