The present study investigates the seasonal changes in lipid components, fucoxanthin (Fx), and functional longchain n-3 (omega-3) polyunsaturated fatty acids (PUFAs) and also evaluates for their antioxidant activity of two tropical brown algae, Nizamuddinia zanardinii and Cystoseira indica, collected from the southeast coast of Iran. Results show a significant amount of fucoxanthin that is possibly due to the specific conditions of sampling area in terms of oxidative stress and the waves of southwest monsoon and thermal stress. Total lipid in October and November was higher compare to rest of the year. The percent of PUFA in N. zanardinii increased coinciding with a period of relative cold weather, but PUFA in C. indica increased in May when the weather is warm. However, in both species, seasonal variation in DPPH radical scavenging activity, CUPRAC, and total phenolic content did not show a particular pattern. A correlation between fucoxanthin content and DPPH radical scavenging activity was evident. Both algal species had higher phenolic content over the peak of maturity and fertility when the plant was tallest (October to December for both species and April for N. zanardinii). In general, variation of these factors in a tropical area such as Oman Sea is different from temperate regions. These changes in many cases are not as tangible, and further investigations are required to assess the variations.