The rarity of polyploidy in animals is often linked to the direct or indirect effects of sex determination mechanisms, a view reinforced by the general association between transitions to unisexuality and polyploidy. However, polyploids are surprisingly uncommon in groups that either engage in bouts of unisexual reproduction or lack sex chromosomes. This study uses a polymerase chain reaction (PCR) amplified region of the ND4-ND5 genes of the mitochondrial genome and allozyme markers to investigate the origins of polyploidy in one group which combines both these attributes: cladoceran crustaceans belonging to the Daphnia pulex (Leydig) complex. Our results show that all of the polyploid clones in this complex originated through interspecific hybridization. A group of melanic polyploid clones were formed through hybridization of three distinct clusters of D. pulicaria or D. melanea with D. pulex, whereas unpigmented polyploid clones originated following hybridization between D. pulex and a more genetically divergent species, D. middendorffiana. This hybridization event was followed by either the ejection or silencing of the maternal nuclear genome, which resulted in the near complete homozygosity of these clones. Our results suggest that the low frequency of hybridization events in animals may be a primary factor constraining the origin of polyploidy in this kingdom.