Zomba District in southern Malawi was reported to have been infested with black-fly in 2006. By the year 2007,the Ministry of Health (MoH) had initiated a larviciding program using Bacillus thuringiensis Israelensis (Bti) tomitigate the effects of black-fly bites. The study aimed at assessing the impact of stratification on black-flythrough monitoring of adult and larvae fly populations following Bit application. The Domasi River was dividedinto three strata and data on the population of black-fly was collected before and after Bit application. Larvamonitoring was done using four different substrate types: nylon strips, rocks, debri and boards on upper andlower sections of the river. Adult monitoring was carried out by human landing catches. All samples collectedwere preserved in 75% alcohol as voucher specimen. It was concluded that stratification of the river did not have statistically significant effect on the impact of Bti on black-fly populations.