Hypoxia and hydrogen sulfide (H2S) intrusion at night contribute to large-scale seagrass mortality events worldwide. Declining water quality has lowered irradiance and enhanced hypoxia in seagrass ecosystems, but linkages between low irradiance and seagrass internal pO2 in situ are not well understood. We examined low irradiance effects on leaf and meristem pO2 dynamics of a dominant tropical seagrass, Thalassia testudinum, using microsensors over multiple diurnal cycles. Further, we determined how O2 dynamics affect H2S intrusion into shoot meristems under low irradiance. Sequential days of low irradiance disrupted internal leaf O2 status in three ways: i) causing a longer lag in morning O2 pressurization, ii) depressing maximum pO2 during the day, and iii) shortening the time where maximum pO2 was sustained into the afternoon. There was a close relationship between leaf and water column pO2 during the day (R2 = 0.93 +/- 0.09); thus, internal O2 dynamics appear more dependent on water column pO2 under low irradiance. The nighttime minimum of leaf and meristem pO2 (1.2 and 0.4 kPa, respectively) were very low and the length of time the meristem sustained hypoxia (< 1.5 kPa pO2) at night was high (9:40 h:min). H2S intrusion into the meristem at night following 24-48 h of shading was persistent, likely the combined effect of limited internal O2 flow without saturating irradiances for photosynthesis, and a breakdown of the sediment oxic microshield. Under low irradiance, more frequent intrusions of H2S to the meristems increases the chances of large-scale seagrass mortality events at night.