We have developed a mid-infrared continuous-wave quantum cascade laser direct-absorption spectrometer (QCLS) capable of high frequency (≥1 Hz) measurements of 12CH4 and 13CH4 isotopologues of methane (CH4) with in situ 1-s RMS precision of 1.5 ‰ and Allan-minimum precision of 0.2 ‰. We deployed this QCLS in a well-studied New Hampshire fen to compare measurements of CH4 isoflux by eddy covariance (EC) to Keeling regressions of data from automated flux chamber sampling. Mean CH4 fluxes of 6.5 ± 0.7 mg CH4 m−2 hr−1 over two days of EC sampling in July, 2009 were indistinguishable from mean autochamber CH4 fluxes (6.6 ± 0.8 mgCH4 m−2 hr−1) over the same period. Mean composition of emitted CH4 calculated using EC isoflux methods was −71 ± 8 ‰ (95% C.I.) while Keeling regressions of 332 chamber closing events over 8 days yielded a corresponding value of −64.5 ± 0.8 ‰. Ebullitive fluxes, representing ∼10% of total CH4 fluxes at this site, were on average 1.2 ‰ enriched in 13C compared to diffusive fluxes. CH4 isoflux time series have the potential to improve process-based understanding of methanogenesis, fully characterize source isotopic distributions, and serve as additional constraints for both regional and global CH4 modeling analysis.