Kappaphycus alvarezii Doty (Doty), commonly known as elkhorn sea moss, is a popular seaweed cultivated globally. It is a well-known source of carrageenan, which is a thickening agent used in food and other industries. Even though different morphotypes of K. alvarezii are reported globally, it has been cultivated and marketed as a single genotype. However, such information is important, especially to produce high-value products such as nutraceuticals. Therefore, this study aimed to evaluate differences in microscopic structure, antimicrobial and antioxidant properties, and total phenolic contents of green and brown morphotypes of K. alvarezii cultivated in Jaffna, Sri Lanka. Except for the colour, there was no significant difference in macroscopic parameters. There was no significant difference observed in cross-sections under the light microscope. Antimicrobial properties of ethanol, methanol and water extracts were evaluated by disc diffusion assay against, Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa. Antioxidant properties and total phenolic contents were determined using 1, 1- diphenyl-2-picrylhydrazyl (DPPH) radical scavenging assay and Folin–Ciocalteau method, respectively. Interestingly, the antibacterial activity, antioxidant properties and total phenolic content of K. alvarezii depend on the morphotype. The green morphotype was rich in total phenolic compounds along with high antibacterial and antioxidant properties. Staphylococcus aureus was the most susceptible bacteria to antimicrobial agents of K. alvarezii and both ethanol and methanol extractions were efficient without significant differences between them in all the assays. The current data suggests better performance of the green morphotype of K. alvarezii as a natural source of antibacterial and antioxidant compounds.