In current research project, taxonomic diversity of two different pathogenic groups of Basidiomycota viz. rust and smut fungi is studied in Khyber Pakhtunkhwa (KP) and adjacent hilly areas of Pakistan. A survey to ten (10) different sampling sites of selected regions was made for three consecutive years. A total of sixty four (64) taxa are identified using both morphological and molecular techniques. This is first time to use molecular markers for taxonomic purpose for selected pathogenic fungi in Pakistan. Among these sixty four (64) taxa, fifty two (52) are rust fungi belonging to fifteen (15) genera of Pucciniales while remaining twelve (12) are smuts of five (05) genera belonging to Urosystales and Ustilaginales. One taxon of rust fungi i.e. Phragmidium pakistanica seems new to science while fifteen (15) taxa including three genera (03) and thirteen (13) species viz. Aecidium viburni, Coleosporium tussilaginis, Macruropyxis sp., Melamspora dimorphospora, Ph. rosae-pimpinellifoliae, Pileolaria pistaciae, Puccinia phaeopoda, P. cnici, P. heraclei, P. polygoni-alpini, P. pollinicola, P. shikotsuensis, Pucciniastrum guttatum, Spherophragmium sp., Uromyces ambiens and three (03) species of smut fungi viz. Sporisorium pulvirulentum, Urocystis narcissi and Ustilago nunavutica are new records for Pakistan. Three (03) rust taxa are reported for the first time from Province KP. In addition to these, six (06) plants are reported as a new host record for the respective fungus. Twenty four (24) rusts and five smuts described in this study have already been reported from Pakistan but here, these are recorded from new localities. This work is first attempt to explore the selected regions of Pakistan thoroughly with respect to rust and smuts. Diversity analysis revealed that members of the Poaceae are most susceptible plants to these pathogens. Similarly distribution analysis via mapping techniques revealed that maximum diversity of rusts is found in Abbottabad district and of smut fungi in Shangla district. Predictive distribution modeling is also performed of selected pathogens to visualize the potential range of disease spread within the country. This work will help in future to set a trend of molecular markers usage in Pakistan for these two groups of fungal pathogens. This data will also help in future taxonomic and phylogenetic studies for comparisons and in up-gradation of checklists of fungal flora of Pakistan. This will help in selection of potential biocontrol agent against various weeds of economically important crops of this agricultural land.