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This study was carried out to determine the spatial variations in malaria mosquito abundance and human biting rate in five villages representing rice-irrigation and savannah ecosystems in Kilosa District, central Tanzania. The study involved five villages namely Tindiga and Malui (wetland/rice irrigation), Twatwatwa and Mbwade (dry savannah) and Kimamba (wet savannah). Indoor mosquitoes were sampled using Centers for Disease Control and Prevention light traps in three houses in each village. Anopheles gambiae s.l. molecular identification was carried out using polymerase chain reaction (PCR). A total of 936 female mosquitoes were collected. About half (46.9%) were malaria mosquitoes (Anopheles gambiae s.l.=28.6%; An. funestus= 18.3%). A total of 161 (60.1%) of the morphologically identified An. gambiae s.l. (268) and subjected to PCR analysis for speciation were genotyped as An. arabiensis. The An. funestus complex mosquitoes were composed of An. funestus funestus and An. rivulorum at the 5:1 ratio. On average, 17.9 Anopheles mosquitoes were collected per village per day. Two-thirds (62.8%) of the malaria mosquitoes were collected in Malui (rice agro-ecosystem) and the lowest number (2.3%) in Twatwatwa (dry savannah ecosystem). The biting rate per person per night for An. arabiensis+An. funestus s.s. was highest in Malui (46.0) and lowest in Twatwatwa (1.67). The parity rate of the An. funestus mosquitoes was lower compared to that of An. arabiensis and none of the mosquitoes was infected with malaria sporozoites. In conclusion, An. arabiensis is the most abundant malaria vector in Kilosa district and its variation is related to the ecological system. The heterogeneity in malaria mosquito abundance and human biting rate could be used to guide selection of locally appropriated control interventions.