A portable Fourier Transform Spectrometer (FTS), model EM27/SUN, is deployed onboard the research vessel Polarstern to measure the column-average dry air mole fractions of carbon dioxide (XCO2) and methane (XCH4) by means of direct sunlight absorption spectrometry. We report on technical developments as well as data calibration and reduction measures required to achieve the targeted accuracy of fractions of a percent in retrieved XCO2 and XCH4 while operating the instrument under field conditions onboard the moving platform during a six week cruise through the Atlantic from Cape Town (South Africa, 34° S, 18° E) to Bremerhaven (Germany, 54° N, 19° E). We demonstrate that our solar tracker typically achieves a tracking precision of better than 0.05° toward the center of the sun throughout the ship cruise which facilitates accurate XCO2 and XCH4 retrievals even under harsh ambient wind conditions. We define several quality filters that screen spectra e.g. when the field-of-view is partially obstructed by ship structures or when the lines-of-sight cross the ship exhaust plume. The measurements in clean oceanic air, can be used to characterize a spurious airmass dependency. ... mehrAfter the campaign, deployment of the spectrometer side-by-side the TCCON (Total Carbon Column Observing Network) instrument at Karlsruhe, Germany, allows for determining a calibration factor that makes the entire campaign record traceable to World Meteorological Organization (WMO) standards. Comparisons to observations of the GOSAT satellite and concentration fields modeled by the European Centre for Medium-Range Weather Forecasts (ECMWF) within the project Monitoring of Atmospheric Composition and Climate – Interim Implementation (MACC-II) demonstrate that the observational setup is well suited to provide validation opportunities above the ocean and along interhemispheric transects.