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Coelacanths were discovered in the Comoros archipelago to the northwest of Madagascar in 1952. Since then, these rare, ancient fish have been found to the south off Mozambique, Madagascar and South Africa, and to the north off Kenya and Tanzania -- but it was unclear whether these are separate populations or even subspecies. Here we show that the genetic variation between individuals from these different locations is unexpectedly low. Combined with earlier results from submersible and oceanographic observations, our findings indicate that a separate African metapopulation is unlikely to have existed and that locations distant from the Comoros were probably inhabited relatively recently by either dead-end drifters or founders that originated in the Comoros.