Marine coccolithophorid phytoplankton are major producers of biogenic calcite, playing a significant role in the global carbon cycle. Predicting the impacts of ocean acidification on coccolithophore calcification has received much recent attention and requires improved knowledge of cellular calcification mechanisms. Uniquely amongst calcifying organisms, coccolithophores produce calcified scales (coccoliths) in an intracellular compartment and secrete them to the cell surface, requiring large transcellular ionic fluxes to support calcification. In particular, intracellular calcite precipitation using HCO3− as the substrate generates equimolar quantities of H+ that must be rapidly removed to prevent cytoplasmic acidification. We have used electrophysiological approaches to identify a plasma membrane voltage-gated H+ conductance in Coccolithus pelagicus ssp braarudii with remarkably similar biophysical and functional properties to those found in metazoans. We show that both C. pelagicus and Emiliania huxleyi possess homologues of metazoan Hv1 H+ channels, which function as voltage-gated H+ channels when expressed in heterologous systems. Homologues of the coccolithophore H+ channels were also identified in a diversity of eukaryotes, suggesting a wide range of cellular roles for the Hv1 class of proteins. Using single cell imaging, we demonstrate that the coccolithophore H+ conductance mediates rapid H+ efflux and plays an important role in pH homeostasis in calcifying cells. The results demonstrate a novel cellular role for voltage gated H+ channels and provide mechanistic insight into biomineralisation by establishing a direct link between pH homeostasis and calcification. As the coccolithophore H+ conductance is dependent on the trans-membrane H+ electrochemical gradient, this mechanism will be directly impacted by, and may underlie adaptation to, ocean acidification. The presence of this H+ efflux pathway suggests that there is no obligate use of H+ derived from calcification for intracellular CO2 generation. Furthermore, the presence of Hv1 class ion channels in a wide range of extant eukaryote groups indicates they evolved in an early common ancestor. The production of calcium carbonate structures by marine organisms has a major influence on the Earth's carbon cycle and is responsible for the eventual formation of sedimentary rocks such as chalk and limestone. The major contributors to marine calcification are the coccolithophores, a family of unicellular algae which surround themselves in calcified plates known as coccoliths. Unlike many other calcifying organisms, coccolithophores produce their calcified structures inside the cell, enabling precise control of this process. However, the other product resulting from the calcification reaction, H+, must be rapidly removed to maintain the pH inside the cell. In this study, we show that coccolithophores possess a voltage-gated H+ channel, which removes H+ rapidly from the cell during calcification and helps maintain a constant pH. We identify the gene encoding this H+ channel, HVCN1, and find that it is a distant relative of those recently identified in animal cells, suggesting that H+ channels may be present in many other types of eukaryote organism. As calcifying organisms may be affected by ocean acidification, the identification of an H+ channel in coccolithophores gives us an important mechanistic understanding of cellular pH regulation during the calcification process, and may give insight into the response of coccolithophores to future changes in ocean pH.