Net ecosystem production is the residual of two much larger fluxes: photosynthesis and respiration. While photosynthesis is a single process with a well-established theoretical underpinning, respiration integrates the variety of plant and microbial processes by which CO2 returns from ecosystems to the atmosphere. Limits to current capacity for predicting ecosystem respiration fluxes across biomes or years result from the mismatch between what is usually measured – bulk CO2 fluxes – and what process-based models can predict – fluxes of CO2 from plant (autotrophic) or microbial (heterotrophic) respiration. Papers in this Thematic Issue and in the recent literature, document advances in methods for separating respiration into autotrophic and heterotrophic components using three approaches: (1) continuous measurements of CO2 fluxes and assimilation of these data into process-based models; (2) application of isotope measurements, particularly radiocarbon; and (3) manipulation experiments. They highlight the role of allocation of C fixed by plants to respiration, storage, growth or transfer to other organisms as a control of seasonal and interannual variability in soil respiration and the oxidation state of C in the terrestrial biosphere. A second theme is the potential for comparing C isotope signatures in organic matter, CO2 evolved in incubations and microbial biomarkers to elucidate the pathways (respiration, recycling, or transformation) of C during decomposition. Together, these factors determine the continuum of timescales over which C is returned to the atmosphere by respiration and enable testing of theories of plant and microbial respiration that go beyond empirical models and allow predictions of future respiration responses to future change in climate, pollution and land use.