Chitin was extracted from the skeleton of Marsupenaeus japonicus shrimp shell waste with a yield of 27.7% of the net weight through three steps namely; deproteinization, decolourization and demineralization. After deacetylation process of extracted chitin, chitosan was produced and represented 55.1% of the extracted chitin. Scanning electron microscope and Fourier Transform Infrared spectroscopy (FTIR) analyses were conducted to characterize the obtained chitin and chitosan. The FTIR analysis revealed different absorption bands within 4000-400 cm^-1 range; by comparison these bands were found to be similar to those of commercial chitin and chitosan and confirmed partial deacetylation in the produced chitosan. Moreover, the antimicrobial activity of commercial and extracted chitin and chitosan were examined against different pathogenic Gram positive, Gram negative bacteria and fungi using agar well diffusion test. Results showed that there was no significant difference p < 0.05 in the antimicrobial activity of the extracted compounds and commercial ones against test pathogens as the extracted compounds recorded inhibition zones ranged from 12 to 23 mm in diameter while the commercial compounds recorded inhibition zones of diameters ranged from 12 to 22 mm only; with Staphylococcus aureus ATCC 25923 being the most affected microbe with inhibition zone of 23 mm produced by extracted chitin, while the lowest zone of inhibition was recorded against Enterococcus faecalis ATCC 29212 with only 12 mm by commercial and extracted chitosan.