Abstract The contribution of the herbaceous stratum to tropical plant diversity is considerable, however this component remains undersampled. We investigated floristic, structural, ecological and conservation issues concerning the herbaceous component of a seasonal deciduous forest associated with granitic rock outcrops in the Cristalino Region, a key area for biodiversity conservation in the Brazilian Amazon. We installed a permanent plot of 1 ha, allocating 10 transect-lines of 20 m each. We identified the sampled individuals, measured height and projection, and verified cover and frequency per species, genera and family. We recorded 86 species, 62 genera and 25 families, with Orchidaceae being the family with the highest species richness. Among the 26 new species added to Cristalino Flora, we included Philodendron deflexum Poepp. ex Schott and Griffinia nocturna Ravenna, the latter ‘Critically Endangered’. Furthermore, the occurrence of G. nocturna in an Amazonian forest matrix is a novelty in this study. The estimate of species diversity according to Shannon-Wiener (H’) was 2.43 nats.ind.-1 (equivalent to 11.37 ± 0.90 IC95% equally common species), and according to Simpson (1/D), 6.82 (± 0.648 IC95%). The rarefaction and extrapolation curves for the diversity estimates tended to stabilize. Although the vegetation on rock outcrops usually presents a high number of endemic species, this pattern was not found in our study area, which can be explained by its continuous occurrence in the forest matrix. The understory of our study area consists in a mixture of floras, being composed mainly of species from the Amazon and/or Cerrado biomes. In view of the current anthropic pressure faced by the southern Amazon, we reinforce the importance of carrying out inventories of its herbaceous communities, since the risk of species loss is even more alarming when considering present undersampling of this component.