The mucoralean zygomycete Parasitella parasitica infects complementary mating types of its host Absidia glauca. This parasitism is characterized by fusion between the partners at infection sites. As a consequence, nuclei of the parasite invade into the host's mycelium. Both types of nuclei undergo frequent recombination. Apart from complementing auxotrophies of the host by genes from the parasite, especially repetitive DNA elements exert remarkable effects in recombinants. Parasitella- specific sequences are efficiently transferred and established in A. glauca, sometimes in copy numbers, exceeding the situation in the donor. In addition, at least one frequent Absidia-specific element (rAg1), lacking from the Parasitella genome, is considerably affected by infection. We have sequenced the genomes of both, host and parasite, and confirmed that the genomes are constituted by 32% (Absidia) and 22% (Parasitella) repetitive DNA. Many of these elements were attributed to known repeat families, some of which are reported as transposable, but approximately 1/3 of all elements are specific for these organisms. Interestingly, both fungi present different repeat specificities. DIRS elements as well as Ginger, MuLE-F, TcMar-ISRm11, TcMar-Tc1, LINE/Jockey and LINE/R1 are specific for the Parasitella parasitica. Transposable elements from the group of endogenous retroviroses as well as LINE/RTE-BovB and Merlin occur exclusively in Absidia glauca.