Target spot is a disease that has caused serious damage to cotton crops. This study was carried out to examine if different cotton genotypes, plant heights and fungicide treatments can be used as tools of an integrated control methods of target spot. The experiment was carried out in the 2014/15 crop season, in cerrado biome of Chapadão do Sul - MS, Brazil. It was used a randomized block design in a 2 × 3 × 3 factorial arrangement with four replicates. The factors were two plant heights (1 and 1.5 m), three cultivars (FMT 701, FM 975, and FM 944), and three fungicide treatments (control, FT1, and FT2). Fungicide treatments consisted of sequential applications of different fungicides of the triazole, strobilurin, and carboxamide groups. Cultivar FM 944 showed lower susceptibility to target spot. The shorter plants exhibited lower disease severity. The fungicides pyraclostrobin + fluxapyroxad and trifloxystrobin + prothioconazole reduced the severity of target spot. Cultivar FM 975 had the highest yield. A higher yield was obtained in the upper stratum than in the lower stratum of the plant.