Research was carried out on performance of larvae capturing traps during larviciding on Domasi River in Zomba. The study was aimed at assessing the impact of Bacillus thuringiensis israelensis (Bti) on black fly larvae colonization of different traps/substrates. Data on black fly larval density on the substrates were collected before and after Bti application. The monitoring was done using three different types of substrates: nylon strips, rocks and debris. The river was divided into three strata and breeding sites were determined. On each stratum all three types of traps/substrates were placed on purposively sampled breeding sites. Bti was applied to the river and its effect on substrate colonization determined. Data analysis included descriptive summaries, correlations, regression and analysis of variance using Microsoft excel and SPSS version 12. The results showed statistically significant differences in larval colonization of substrates. Substrates were capturing different densities before and after Bti application. Rock and Debris captured relatively high densities in both situations though the densities were much high before application. Nylon string had lower colonization. This study indicates that the performance of the different substrates at capturing larval density is affected by Bti due to its killing effect hence a consideration has to be made as to which substrate to use in larval monitoring.