Seaweed farming has been the cause of introductions of non-indigenous seaweed species and genotypes throughout the world. In Zanzibar, Tanzania, foreign genotypes of Eucheuma denticulatum were introduced for farming purposes in 1989, and in recent years a spread of non-indigenous haplotypes has been reported. The current study aimed to investigate the presence and extent of introduced and native haplotypes of E. denticulatum as well as their relative frequencies, to obtain the severity of the spread of cultivated seaweed and the current state of the native populations. The results show that all investigated sites are dominated by the introduced South-east Asian haplotypes, even where seaweed farming has never occurred. As the frequencies of East African haplotypes are remarkably low, this shows a shift from native to introduced E. denticulatum. This shift may, at least in part, be caused by earlier overharvest of natural seaweed populations, and indicates a cryptic invasion of the introduced haplotypes at the potential cost of the recovery of the native haplotype populations.