Research on fern ecology has gained attention in the last decade, yet there is a paucity of information on the comparison of ferns communities across continents. This study focused on comparing the ferns community assemblages in some tropical forests of Malaysia and Nigeria, thereby assessing the patterns of species richness (SR) and phylogenetic diversity(PD) in relation to the bioclimatic drivers across the continents. The diversity and taxonomic compositions of ferns were assessed using 180 plots of 10 m x 10 m in each country. The species richness and other diversity indices were determined using the combined forests data for each country and for the individual forests. Also, the phylogenetic diversity of the ferns was assessed using the genus-based molecular sequences downloaded from the GeneBank. The patterns of the ferns SR and PD in the two countries as driven by some bioclimatic factors were evaluated using the regression analysis. The observed and rarefied–extrapolated fern species richness is significantly higher in Malaysian forests than in Nigerian forests. Also, the other diversity indices are significantly higher in Malaysian forests except for the Shannon index which showed no significant difference between the two biogeographic regions. There is a very low similarity (7.41%) in the taxonomic composition of ferns between the two biogeographic areas, although the similarity in composition increased with increasing taxonomic levels (species: 7.41%, genus: 12.77%, family: 70.96%). Terrestrial and epiphytic ferns are more dominant than the other life forms in the two countries. The precipitation variables drive the phylogenetic structure of ferns in Nigeria whereas both precipitation and temperature variables drive the phylogenetic structure of ferns in Malaysia. This indicates that ferns assemblages in Nigeria and Malaysia are driven by both climatic variables. Besides, we also hypothesize that these observed differences could be due to other historical and evolutionary processes.