Shigella flexneri is the main causative agent of shigellosis commonly distributed in developing countries with high morbidity and mortality rates. This study aimed to examine the presence of Shigella species in Sudanese currency notes using both traditional and molecular techniques. One hundred thirty five currency notes were collected and their contaminants were isolated and identified conventionally and genetically using 16S rRNA gene amplification and sequencing. Eight isolates were identified as Shigella species in different notes, and 3 of them were resistant to penicillin, kanamycin and nitrofurantoin. One S. flexneri isolate has insertion mutation of guanine nucleotide at position 730 of life's essential gene 16S rRNA which known evolutionarily to be stable gene. Banknotes are highly circulating items and therefore, appropriate measures such as regular replacement of the dirty notes with new papers are necessary to protect peoples from being infected with drug resistant pathogens.