Interaction of aquatic stages of coexisting mosquito species may have significant influence on resulting adult mosquito populations. We used two coexisting species, Anopheles gambiae s.s. and Culex quinquefasciatus to investigate whether third instars of one species consumed first instars of the other. First instars of one species were readily consumed by a third instar of the other species irrespective food quantity. DNA of Cx. quinquefasciatus was detected in the eight An. gambiae s.s. third instars presumed to have consumed at least one Cx. quinquefasciatus first instar. Likewise, DNA of An. gambiae s.s. was detected in five of eight Cx. quinquefasciatus third instars presumed to have consumed at least one An. gambiae s.s. first instar. A small number of dead first instars was found in the controls indicating that some larvae in the treatment group may have been consumed after they had died. These findings suggest that intraguild predation between the two species may be common in nature and that it is a facultative process that is not induced by food shortage. The findings further suggest that polymerase chain reaction could be a useful technique in the study of this phenomenon in natural habitats.