The Mexican fruit fly Anastrepha ludens (Loew) (Diptera: Tephritidae) is a polyphagous pestiferous insect with a geographical range encompassing highly variable environmental conditions. Considering that cryptic species have been recently found among South American representatives of the same taxonomic group as A. ludens, we tested whether or not some populations of A. ludens have evolved assortative mating as an isolating mechanism that maintains intrapopulation genetic differences and behavioral adaptations to local conditions. Males and females stemming from widely separated locations with similar environmental conditions and males and females stemming from populations within individual-flight range, but collected in different hosts (a native and an exotic one), mated randomly amongst themselves when placed in a field cage. Despite the fact that sibling males and females from two distinct populations also mated randomly amongst themselves, siblings engaged in significantly longer copulations than non-siblings, indicating that perhaps adults discriminated mates with similar genetic compositions. Our results have important practical implications as A. ludens is the most devastating pest of citrus in Mexico and Central America, and large-scale releases of sterile flies are used to control it.