Damage by the tropical warehouse moth, Ephestia cautella (Walker) to stored plant products especially dried cocoa beans is enormous. This is expressed in holing with frass and webbing of the beans leading to nutritional loss; turning the valuable commodity into powder and reducing the value in the export-import market. Effective management of the pest is contingent upon correct identification and bioecological expressions in relation with the host(s) and other environmental influences. Therefore, the morphological traits (phenotypic) variability between sexes and populations of E. cautella across different locations in Southwestern Nigeria were investigated with a view to identifying the population structure of E. cautella in the region. Thirty-two ecotypes of E. cautella (16 male; 16 female) populations (n = 10/ecotype) were evaluated for eight morphometric traits including forewings (length and width), hind-wings (length and width), body length, antenna length and abdominal dimension (length and width). Significant variations (P ≤ 0.05) occurred among the 32 E. cautella ecotypes for the eight measured traits with respect to sexes, locations and the interactions of the two sources of variation (sex by location). By magnitude, the females had significantly (P ≤ 0.05) higher mean for the fore and hind wings (length and width), body length and abdominal dimension; however, the antenna length was longer in males than in females' samples. The overall mean Gower genetic distance for the 32 E. cautella ecotypes was 0.656, with the range of 0.273 to 0.968. At 0.1 level of similarity index, four clusters (I, II, III, IV) emerged; with the membership of 7, 8, 12, and 5 respectively. This study showed that four ecotypes of E. cautella exist in southwestern Nigeria with sex by location assessment and this can be useful in control programmes of the pest.