We examined sperm storage patterns of doubly mated females in a species of tephritid fly (Anastrepha suspensa (Loew) [Diptera:Tephritidae]) with four sperm storage organs and an unusually complex reproductive system to elucidate possible reproductive arenas in which sexual selection can or has played a role in sperm competition and cryptic female choice and to predict effects on paternity outcomes. The duration of copulation with each male of doubly mated female flies was recorded and the sperm storage organs were dissected to determine the location and identity of each male's sperm (by microsatellite polymerase chain reaction) and its relative quantity. Short copulations with the first male generally resulted in little transfer of sperm and predicted the length of time spent in second copulations, resulting in disproportionate sperm storage from second copulations. For doubly mated females, most storage organs contained sperm from second males only, although the fertilization chamber often contained sperm from both males (allowing for possible sperm competition). Long-term storage organs (spermathecae) always contained sperm from single males exclusively possibly limiting opportunities for sperm competition. Our data provide a mechanism for second male precedence without invoking sperm competition, and caution that paternity patterns must be critically interpreted with inclusion of information on sperm storage patterns.