There are a number of Anopheles species playing either primary or secondary roles in malaria transmission. Hence, understanding the species composition, their bionomics, and behaviors are all important in designing and implementing vector control intervention tools. Moreover, accurate identification of different species is vital. This study aimed to assess species composition, sporozoite infection rate, and blood meal origins of malaria mosquitoes in two malaria-endemic villages of Boreda district in Gamo zone, southwest Ethiopia. Thirty houses, 20 for Centers for Disease Control and Prevention (CDC) light traps and 10 for Pyrethrum Spray Catches (PSC), were randomly selected for bimonthly mosquito collection from October 2019 to February 2020. Enzyme-linked-immunosorbent assay (ELISA) test was done to detect the blood meal origins and circumsporozoite proteins (CSPs). The entomological inoculation rate (EIR) was calculated by multiplying the sporozoite and human biting rates from PSCs. Anopheles gambiae and An. funestus complexes were further identified into species by polymerase chain reaction (PCR). Anopheles species with some morphological structures confusing with An. gambiae or An. funestus complexes were father confirmed by PCR. A total of 15 Anopheles species were documented, of which An. demeilloni was the dominant one. Only An. arabiensis was positive for P. falciparum CSP. The overall P. falciparum CSP rate of An. arabiensis was 0.54%. The overall estimated P. falciparum EIR of An. arabiensis from PSC was 1.5 infectious bites/person/five months. Of the 145 freshly fed Anopheles mosquitoes tested for blood meal source, 57.9% (84/145) had bovine blood meal, 22 (15.2%) had human blood meal origin alone and 24 (16.5%) had mixed blood meal origins of human and bovine. An. demeilloni mainly fed on bovine blood (102/126 = 80.9%). Among 420 morphologically classified An. demeilloni, 11 (2.6%) were confirmed as An. lessoni (one of the An. funestus complexes) by PCR. A substantial number of morphologically classified An. salbaii, An. maculipalpis and An. fuscivenosus were found to be An. arabiensis by PCR. Regardless of the high diversity of Anopheles mosquitoes, An. arabiensis is playing the primary role in malaria transmission. Morphological misclassification of species could be a challenge in malaria mosquito monitoring and surveillance, and hence it should be supported by more sensitive techniques for confirmation.