Mosquito ecology is influenced by wetness in the environment. In 2011-2014, a rise in waters of Lake Baringo resulted in unprecedented flooding that inundated over 88km2 of the shoreline. A longitudinal study carried out from October 2012-October 2013 assessed mosquito abundance and diversity in two habitats. A total of 386,624 mosquitoes were captured, 89% from flooded shoreline and 11% from swampy habitat. Family Culicinae constituted 10 genera. Mansonia dominated the catches with 98% from flooded shoreline and swampy habitat 2%. Genetic sequences of Aedes albopictus species was identified and reported for the first time in the basin. Diversity index was higher in swampy habitat (Simpson Diversity Index=0.56), compared to flooded shoreline (Simpson diversity index =0.13). Future recurring floods will result in drastic changes of the ecology and could lead to emergence and reemergence of more species.