Phylogeny investigation relying on chloroplast genome sequence is an established approach in differentiation between plants derived from related ancestors. In this study, we compared the phylogenetic tree resulted from chloroplast genome sequences to phylogenetic tree generated from pollen grains features of ten taxa belonging to the Caesalpinioideae sub-family, grown in Egypt. Chloroplast genome sequences of taxa under investigation, retrieved from the National Center for Biotechnology Information (NCBI), were used to generate a phylogenetic tree using RStudio^® software. Pollen grain features were investigated using the Scanning Electron Microscope (SEM) and data were combined in a numerical cluster to compose a phylogenetic tree. Both phylogenetic trees, originating from chloroplast genome sequences and pollen grains features in our study indicated high similarity in relatedness between taxa. Our results suggest the utilization of both pollen grains features and molecular characteristics in discrimination between plants stemming from common ancestors. The novelty of this work lies in comparing similarities and differences of the investigated species through combining their pollen and molecular characteristics altogether. The identification key of the investigated species, reported in this manuscript, is hoped to be a reliable approach and can be utilized by taxonomists for taxa identification in the future.