Microsatellite loci have been developed for three undescribed species discovered at hydrothermal vents on the East Scotia Ridge (ESR) in the Southern Ocean: a yeti crab, Kiwa sp. (Kiwaidae), a species of peltospiroid gastropod and a vent limpet, Lepetodrilus sp. (Lepetodrilidae). Nine, twelve and fourteen loci were developed for the three species respectively, with two loci deviating significantly from Hardy–Weinberg expectations. Observed heterozygosity ranged from 0.08 to 1 (means of 0.62, 0.44 and 0.63 for the three species respectively). These loci are being used to determine connectivity between vents at the northern and southern end of the ESR and between the ESR and the Kemp Caldera, a submerged part of the South Sandwich Island chain. These data will be crucial in understanding the ecology of the first hydrothermal vent communities discovered in the Southern Ocean.