In regions characterized by arid seasons, such as the Mediterranean basin, soil moisture is a major driver of ecosystem CO2 efflux during periods of drought stress. Here, a rain event can induce a disproportional respiratory pulse, releasing an amount of CO2 to the atmosphere that may significantly contribute to the annual ecosystem carbon balance. The mechanisms behind this pulse are unclear, and it is still unknown whether it is due to the stimulation of autotrophic, heterotrophic and/or inorganic CO2 fluxes. On the Mediterranean island of Pianosa, eddy flux measurements showed respiratory pulses after rain events following prolonged drought periods, which occurred in the summer of 2003 and 2006. To investigate the mechanisms of this observed enhanced respiration fluxes and partition of the soil CO2 sources, two water manipulation experiments were performed. The first was designed to estimate the effect of soil rewetting on soil CO2 efflux, in the different ecosystem types existing on the island (i.e. woodland, ex-agricultural and Mediterranean shrubland). The second was a soil CO2 partitioning experiment to investigate the relative contribution of inorganic and organic CO2 sources to soil respiration, under dry and wet soil conditions. Our results suggest that the pulse in the CO2 efflux is primarily due to the enhancement of heterotrophic respiration, likely caused by the degradation of easily decomposable substrates, accumulated in soils during the dry period. In fact, the vegetation at the site was senescent and did not play any significant role in CO2 exchange, as suggested by the absence of diurnal CO2 uptake in eddy covariance measurements. In addition, soil rewetting did not significantly enhance inorganic CO2 efflux.