Collapse of the West Antarctic Ice Sheet (WAIS) would raise global sea level by ∼3.3–5 m. Ice-sheet models and geological data suggest at least one collapse has happened during the last 1.1 Ma, and some scenarios of future climate change predict a collapse within the next two centuries. A complete WAIS collapse would open shallow seaways across West Antarctica, potentially enabling exchange of animals between West Antarctic seas. We investigated biological evidence for past connectivity between different regions of Antarctica by comparing the composition of modern bryozoan assemblages from the continental margin around Antarctica. Surprisingly, we found most similarity between two areas which are not currently connected – the shelves of the Weddell Sea (WS) and Ross Sea (RS). We evaluated three hypotheses to explain this and conclude that bryozoans most likely dispersed through a trans-Antarctic seaway that opened in response to a WAIS collapse and connected the WS and RS shelves. These bryozoans must have survived glaciations(s) during subsequent ice ages in refuges, whereas they were wiped out in most other regions of the Antarctic shelf. After the last glacial period, bryozoan assemblages could freely disperse between many of the regions we examined (e.g. Antarctic Peninsula and South Shetland Islands), which has allowed recolonization of areas in which bryozoans had been eradicated during the last ice age. For the bryozoans on the WS and RS shelves to be more similar than those which are in close proximity means the trans-Antarctic seaway may have been as late as the last few interglacials. Current rates of warming are exceptional compared with the near past glacial cycles so our study, the strongest faunal evidence of WAIS collapse during the recent geological past, thus supports predictions of a near future WAIS collapse (with considerable global sea level implications) and resultant future major faunal exchanges.