Antibiotic resistance of cyanobacteria has been a global threat to public health. The widespread presence of cyanobacteria in aquatic environments exposes them to antibiotic contamination. The cyanobacteria are also in direct contact with pathogenic bacteria containing Antibiotic-Resistance Genes (ARGs) that gives them these characteristics. The study aims to the presence of some ARGs in locally isolated cyanobacteria species, Spirulina laxa, Chroococcus minutes, Oscillatoria princeps, Oscillatoria proteus, Oscillatoria terebriformis, Lyngbya epiphytica, and to compare the presence of these genes in two pathogenic bacteria, Escherichia coli and Klebsiella pneumoniae. The results revealed the presence of The ampicillin (Ap) and erythromycin (Em) resistance genes were detected in five algal samples. Meanwhile, the chloramphenicol (Cm) and gentamicin (Gm) resistance genes were apparent in only two species. Genes encoding resistance towards kanamycin (Km) and spectinomycin (Sp) were recorded in three specimens. The results also documented that E. coli possessed the resistance genes for four antibiotics: Ampicillin (Ap), Erythromycin (Em), Gentamicin (Gm), and Kanamycin (Km), whereas K. pneumoniae was resistant towards three anti-biotics: Ampicillin (Ap), Gentamicin (Gm), and Kanamycin (Km). The results show that there are a match in antibiotic resistance genes in both cyanobacteria and pathogenic bacteria. suggesting the possibility that cyanobacteria could acquire ARGs from the environment through horizontal gene transfer. Thus, freshwater cyanobacteria may play an important role in the prevalence of ARGs in their environment.