This study is the first contribution towards the estimation of paleoatmospheric carbon dioxide concentration (pCO2) from the paleoequatorial late Aptian Crato Formation (Santana Group, Araripe Basin, NE Brazil) based on stomatal numbers. Cuticular and epidermal silicon replicas of Pseudofrenelopsis capillata Sucerquia, Bernardes-de-Oliveira & Mohr (Cheirolepidiaceae, Coniferales) were observed under scanning electron microscopy to analyze their stomatal frequency and distribution for paleoatmospheric and paleoenvironmental inferences. Stomatal counting yielded a mean stomatal density (SD) and stomatal index (SI) of 68.8 mm−2 and 6.7. Based on the mean SI value of four modern nearest living equivalent (NLE) conifer species, the stomatal ratio (SR) was calculated to be 1.4. The paleoatmospheric pCO2 range was estimated to be between 514.9 ppmv (Recent standardization) and 1029.8 ppmv (Carboniferous standardization). These values were found to be consistent with results from the literature based on other latitudes in the Early Cretaceous and were discussed in the light of the paleoenvironmental context that prevailed around the peri-equatorial Crato paleolake, including the occurrence of stomatal clustering in the leaves of P. capillata.