How unisexual animals eliminate deleterious mutations to avoid dead ends is one of the most interesting puzzles in evolutionary genetics. Incorporation of microchromosomes derived from exogenous sperm had been observed in gynogenetic animals, but little is known about their detailed process and hereditary fate. Here, we show a stable genome incorporation case in an artificial clone F of gynogenetic gibel carp (Carassius gibelio). A total of 12 exogenous DNA fragments were screened through a read depth-dependent comparison strategy and confirmed to be specific to the clone F and the paternal blunt snout bream (Megalobrama amblycephala Yin) by SCAR (sequence characterized amplified regions) marker detection. Moreover, these sperm-derived DNA fragments were not detected in some samples in early gynogenetic generations, but they were found to exist in all examined individuals through artificial gynogenetic selections of 13 generations, implying that they might have stably incorporated into the genome of clone F. Furthermore, chromosome localization and sequence characterization indicate that the largest fragment CgA22_34 is derived from blunt snout bream non-LTR retrotransposon and durably incorporated into only one of three homologous chromosomes of gibel carp clone F. Our results suggest that the incorporated sperm-derived DNA fragments by allogynogenesis should increase genetic diversity and introduce new traits into unisexual animals which will benefit genetic breeding of gibel carp. During the process, transposable elements (TEs) may play significant roles in shaping the genome structures. Simultaneously, the incorporated DNA fragments are able to be used as genetic markers to perform selective breeding programs in aquaculture practices of gibel carp.