The noncellular peritrophic matrix (PM) that forms around the food bolus in the midgut of many arthropod species may influence the fate of ingested microbes. In mosquitoes, PMs have been identified in the pupal as well as larval and adult stages. In pupae, the PMs surround the meconium, the sloughed larval midgut epithelium. Meconial PM1 (MPM1) forms early in the pupal stadium, and a second meconial PM (MPM2) sometimes forms around the time of adult emergence. A recent study suggests that MPMs contribute to the sterilization of the adult midgut by sequestering microorganisms ingested during the larval stage, which, along with remaining meconial material, are egested after adult emergence. We have compared MPM1 formation and patterns of meconial degeneration in representative species in five mosquito genera and identified a temporal association between MPM1 formation, meconial degeneration, and apolysis. Ultrastructural study of MPM1 and MPM2 in Aedes aegypti (L.) revealed that MPM1 seems to be structurally different from either the larval or adult PMs, whereas MPM2 more closely resembles PM formed around a bloodmeal in adult females. Our results are consistent with the microbial sequestration role.