Understanding whether marine calcifying organisms may acclimatise to climate change is important with regard to their survival over the coming century. Due to cold waters having a naturally higher CO2 uptake, the Southern Ocean provides an especially good opportunity to study the potential impact of climate change. In 2011, a new cheilostome bryozoan species—Chiastosella ettorina sp. nov.—was dredged from Burdwood Bank, Southern Ocean, at 324–219-m depth during the Nathaniel B Palmer Cruise. This species had previously been collected in 1902 from the same area at 100-m depth, but was incorrectly identified as Chiastosella watersi, an encrusting species from New Zealand. The availability of samples of the same species, from the same general location, but collected 109 years apart allowed us to investigate morphological modifications potentially arising from environmental changes. We found a significant difference in zooid size, with the oldest and shallowest specimens having smaller zooids than the recently collected deeper specimens. This difference in zooid size appears to be unrelated to known sources of environmental variation such as temperature and salinity, and it could represent the extremes of the zooid size range of C. ettorina. An alternative explanation is that acidifying waters may have caused zooids to grow more slowly, resulting in a final larger size.