The objective of this study was to characterize the genetics of second generation (F ) koi Cyprinus carpio × goldfish Carassius auratus hybrids. Spermatozoa produced by a novel, fertile F male were found to be diploid by flow-cytometric analysis. Backcross (F female × C. carpio male and C. carpio female × F male) juveniles were triploid, confirming that female and male F hybrids both produced diploid gametes. The vast majority of surviving F juveniles was diploid and small proportions were aneuploid (2·1n-2·3n and 3·1n-3·9n), triploid (3n) and tetraploid (4n). Microsatellite genotyping showed that F diploids repeated either the complete maternal or the complete paternal genotype. Fish with the maternal genotype were female and fish with the paternal genotype were male. This demonstrates that F diploids were the result of spontaneous gynogenesis and spontaneous androgenesis. Analysis of microsatellite inheritance and the sex ratio in F crosses showed that spontaneous gynogenesis and androgenesis did not always occur in equal proportions. One cross was found to have an approximate equal number of androgenetic and gynogenetic offspring while in several other crosses spontaneous androgenesis was found to occur more frequently than spontaneous gynogenesis.