The relationship between pheromone composition and mitochondrial haplotype clades was investigated by coupling DNA analyses with pheromone identification and male mate searching behavior among different geographic populations of Busseola fusca. The within-population variations in pheromone blend were as great as those observed between geographic populations, suggesting that the female sex pheromone blend was not the basis of reproductive isolation between the geographic clades. Furthermore, while data from wind tunnel experiments demonstrated that most of the tested males were sensitive to small variations in pheromone mixture, there was considerable within-population variability in the observed response. The study identified a new pheromone component, (Z)-11-hexadecen-1-yl acetate, which when added to the currently used three-component synthetic blend resulted in significantly higher traps catches. The new recommended blend for monitoring flight phenology and for timing control measures for optimal efficacy of B. fusca is (Z)-11-tetradecen-1-yl acetate (62%), (E)-11-tetradecen-1-yl acetate (15%), (Z)-9-tetradecen-1-yl acetate (13%), and (Z)-11-hexadecen-1-yl acetate (10%).