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Deep-sea cold seeps support diverse communities that include vestimentiferan tubeworms of the genus
Escarpia
. To investigate population structure to understand how deep-sea communities are established, several polymorphic microsatellites were developed using 454 pyrosequencing. Eleven and sixteen loci were identified in
Escarpia laminata
(n = 129) and
Escarpia southwardae
(n = 80). Additionally, the amplification of microsatellites is expected to be successful in closely related species and can help resolve their phylogenetic relationships. Nine of the
E. laminata
loci were amplified across three
Escarpia
species (n = 229). Four of the twenty-eight loci deviated from Hardy–Weinburg Equilibrium and no linkage disequilibrium was found in the loci tested here.