Malaria vector control in Ethiopia has a history of more than 50 years, but malaria remains a major cause of morbidity and mortality in Ethiopia. Thus, targeting the control program on the larval stage is of paramount importance. This study aimed to characterize the aquatic habitats of vector mosquito larvae associated with micro-dams. Cross-sectional larval survey was conducted on six micro-dams in Tigray, Northern Ethiopia in 2005/06. The study area on each dam was divided into eight zones. Immature stages of mosquitoes were collected using standard dippers. The physico-chemical characteristics of the aquatic habitats were measured onsite. A total of 301 aquatic habitats were surveyed for mosquito larvae; in 32.56% (n=301) only Anopheles, in 27.91% only Culex, both genera were found mixed in 21.59% and no mosquito larvae were found in 17.94%. The findings depicted that dissolved oxygen (r = 0.34, p =0.04), pH (r = 0.35, p =0.03), conductivity (r = 0.36, p =0.03), vegetation (F = 3.54, p =0.002), microhabitat (F = 2.65, p =0.04), fauna and bottom surface of the water body were positively associated and important in explaining the presence and abundance of Culex. On the other hand, dissolved oxygen (r = 0.39, p =0.02), pH (r = 0.42, p =0.008), vegetation (F = 5.6, p =0.000), water transparency (F = 2.72, p =0.00), rainfall (F = 2.22, p = 0.027) and fauna were positively associated and important in explaining the presence and abundance of Anopheles. The findings of this study suggest that both biotic (vegetation and fauna) and abiotic (chemical and physical) factors play a significant role in larvae's habitat preference in both Culex and Anopheles.