Family Malvaceae has been traditionally subjected to several taxonomic approaches regarding their taxon relationships and divisions. With the rapid advancement of PCR-based methods and DNA sequence information, taxonomists now have the opportunity to shift from traditional systems of classification to more recent systems. Molecular studies of Malvaceous taxa have provided new opinions about the grouping and phylogeny of these taxa. This work involved molecular analyses of twenty-three Malvaceae species. Three molecular techniques were used, namely, inter simple sequence repeat (ISSR), sequence-related amplified polymorphism (SRAP), and internal transcribed spacer (ITS), to investigate the relationships between the studied taxa. Phylogenetic relationships were constructed using Molecular Evolutionary Genetics Analysis and Phylogenetic Analysis Using Parsimony (MEGA and PAUP) software. The results of this investigation revealed 301 molecular characteristics (78 ISSR and 223 SRAP bands) between the taxa. These data support the taxonomic view of the Malvaceae s.l.subfamilies in the Angiosperm Phylogeny Group system of plant classification (APG systems).