The negative landform of sinkholes provides belowground level refugia for a high diversity of forest species compared to the forests on the surface of surrounding karst plateaus in southeastern China. Bryophyte diversity in sinkhole forests is also likely to be high. In this study, bryophytes of an underground forest sinkhole (UFS), and two forests (Forest Karst Mountain 1; FKM1) and (Forest Karst Mountain 2; FKM2) on the surface of the karst plateau were compared to understand the role of the sinkhole forest in the conservation of bryophyte diversity and the relationships between bryophyte diversity, environmental factors, and soil nutrients. Significantly more bryophyte taxa were recorded from the sinkhole forest (71 taxa, 36 genera, 23 families) than those in the forest on the plateau surface, which was the closest to the sinkhole (FKM1; 29 bryophyte taxa, 16 genera, 12 families), and even fewer bryophytes were found in the forest more distant to the sinkhole (FKM2; 22 taxa, 17 genera, eight families). Twenty-four liverwort taxa were collected from the sinkhole forest, two from the closest surface forest (FKM1) and none from the furthest surface forest (FKM2). Ninety-three percent of the bryophytes in karst mountain sinkhole were not found on surface forest. The diversity index trend was as follows: UFS > FKM1 > FKM2, and the evenness index trend was in the opposite direction as follows: UFS < FKM1 < FKM2. The beta diversity showed that the Jaccard index among the three forests was 0–0.25, reflecting a huge difference between the sinkhole forest and the two surface forests. Canonical correspondence analysis showed that light was the most important factor affecting the distribution of bryophytes in the sinkhole forest, while temperature and humidity were key factors for the distribution of bryophytes in the two surface forests. Further, soil parameters, namely, soil organic carbon, total nitrogen, total phosphorus, total potassium, alkali-hydrolyzed nitrogen, and available phosphorus changed gradually from UFS to FKM1 and to FKM2. The sinkhole forest, located in a landform with the unique negative topography enclosed by cliffs, and with a complex microenvironment, provides a natural refuge for bryophyte species in areas where forests have been negatively impacted by karst rocky desertification. © The Author(s) 2020.