ORIGINAL PAPER Conservation implications of significant population differentiation in an endangered estuarine seahorse T. K. Mkare 1,2 • B. Jansen van Vuuren 1 • P. R. Teske 1 Received: 25 August 2016 / Revised: 11 January 2017 / Accepted: 24 January 2017 / Published online: 18 February 2017 Ó Springer Science+Business Media Dordrecht 2017 Abstract The spatial distribution of a species’ genetic diversity can provide insights into underlying evolutionary, ecological and environmental processes, and can contribute information towards the delineation of conservation units. The Knysna seahorse, Hip- pocampus capensis, is endangered and occurs in only three estuaries on the warm-tem- perate south coast of South Africa: Knsyna, Keurbooms and Swartvlei. Population sizes in the latter two estuaries have been very small for a prolonged period of time, and the populations residing in them may thus benefit from translocations as a means of increasing population sizes and possibly also genetic diversity. However, information on whether these three estuaries constitute distinct conservation units that warrant separate manage- ment is presently lacking. Here, we used genetic information from mitochondrial (control region) and nuclear microsatellite loci to assess the genetic diversity and spatial structure across the three estuaries, and also whether translocations should be included in the management plan for the Knysna seahorse. Although each population had a unique combination of alleles, and clustering methods identified the Swartvlei Estuary as being distinct from the others, levels of genetic admixture were high, and there was no evidence for reciprocal monophyly that would indicate that each estuary has a unique demographic Communicated by Angus Jackson. This article belongs to the Topical Collection: Coastal and marine biodiversity. Electronic supplementary material The online version of this article (doi:10.1007/s10531-017-1300-5) contains supplementary material, which is available to authorized users. & P. R. Teske pteske101@gmail.com 1 Molecular Zoology Laboratory and Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, Johannesburg, South Africa 2 Present Address: Kenya Marine and Fisheries Research Institute, P.O. Box 81651–80100, Mombasa, Kenya 123 Biodivers Conserv (2017) 26:1275–1293 DOI 10.1007/s10531-017-1300-5