1. Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109-8099, USA
2. Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
3. These authors contributed equally to this work.

Correspondence to: Mark R. Swain^1,3 Correspondence and requests for materials should be addressed to M.R.S. (Email: Mark.R.Swain@jpl.nasa.gov).

Molecules present in the atmospheres of extrasolar planets are expected to influence strongly the balance of atmospheric radiation, to trace dynamical and chemical processes, and to indicate the presence of disequilibrium effects. As molecules have the potential to reveal atmospheric conditions and chemistry, searching for them is a high priority. The rotational–vibrational transition bands of water, carbon monoxide and methane are anticipated to be the primary sources of non-continuum opacity in hot-Jupiter planets^{1, 2, 3}. As these bands can overlap in wavelength, and the corresponding signatures from them are weak, decisive identification requires precision infrared spectroscopy. Here we report a near-infrared transmission spectrum of the planet HD 189733b that shows the presence of methane. Additionally, a resolved water vapour band at 1.9 m confirms the recent claim⁴ of water in this object. On thermochemical grounds, carbon monoxide is expected to be abundant in the upper atmosphere of hot-Jupiter planets, but is not identifiable here; therefore the detection of methane rather than carbon monoxide in such a hot planet^{5, 6} could signal the presence of a horizontal chemical gradient away from the permanent dayside, or it may imply an ill-understood photochemical mechanism that leads to an enhancement of methane.