Multi-drug resistant pathogens are a leading cause of human morbidity and mortality all over the world. This study aimed at isolating actinomycetes from the soils of Menengai crater and characterizing selected actinomycetes using morphological, biochemical, and molecular techniques. The study involved isolation of actinomycetes using Starch Casein (SC), Luria Bertani (M1) and Starch Nitrate (SN) agar media. The isolated actinomycetes were characterized using morphological and biochemical techniques. The screening for antibiotic activity was carried out via primary screening using perpendicular method and secondary screening using agar plug technique against Staphylococcus aureus (ATCC 25923), Streptococcus pneumoniae (ATCC 49617), Enterococcus faecalis (ATCC 29212), Escherichia coli (ATCC 25922), Pseudomonas aeruginosa (ATCC 27853), Proteus vulgaris (ATCC 49990), Alternaria citri (ATCC 1015), Candida albicans (ATCC 10231), Fusarium oxysporum (ATCC 16608) and Ustilago maydis (ATCC 14826). The best actinomycetes based on size of inhibition and broad spectrum of activity coded PAN 25, PAN 41, PAN 75 and PAN 110 were selected for further bioassay. Extraction of antibiotics was carried out using ethyl acetate. The selected actinomycetes were characterized using molecular technique that involved extraction of 16S rRNA gene, PCR and phylogenetic studies. The data obtained was analyzed using Statistical Package of Social Sciences (SPSS) version 25 software. The number of the isolated actinomycetes varied significantly (F=3.315 P=0.04218). There was no significant difference in the zones of inhibition between the isolates PAN 25, PAN 41, PAN 75 and PAN 110 (F=0.8928 P=0.5431). In addition, there was no significant difference in the zones of inhibition between the extracted antibiotics (F=1.726424 P=0.126281). The 16S rRNA gene sequence and nucleotide BLAST from NCBI revealed that isolate PAN 25 had similarity with Streptomyces variabilis, isolate PAN 41 (S. indiaensis), isolate PAN 75 (S. luteogriseus strain ZG728) and isolate PAN 110 (S. acrimycini strain K30). Menengai crater had actinomycetes that inhibited growth of the selected actinomycetes. There is need of isolating actinomycetes from other unique regions in Kenya. Large scale production of antibiotics from the selected actinomycetes need also to be carried out.