Microalgae are potential sources of bioactive compounds that have health promoting effects due to the abundant presence of flavonoids and polyphenols. The goal of this study was to investigate the chemical profiles of microalgae extracts from Nannochloropsis sp. and Spirulina sp. Total phenolic content (TPC), total flavonoid content (TFC), and antioxidant activity (DPPH) were measured. Nannochloropsis sp. had a significantly higher TPC value than Spirulina sp. (58.43 ± 0.85 mg GAE/g DW vs. 19.64 ± 0.52 mg GAE/g DW, p < 0.01) and a significantly higher TFC value than Spirulina sp. (79.87 ± 0.12 mg QE/g DW vs. 11.19 ± 0.07 mg QE/g DW, p < 0.01). Nannochloropsis sp. also exhibited a greater percentage of DPPH inhibition compared to Spirulina sp. (EC50 0.195 ± 0.007 mg/mL vs. 0.613 ± 0.003 mg/mL, p < 0.01). TPC and TFC were negatively correlated with the EC50 of DPPH antioxidant inhibition activity (-0.956, p = 0.003, and –0.899, p = 0.015, respectively). These negative correlations indicate that polyphenol compounds are the major contributors to the antioxidant activity observed in this study. Further analysis is needed to determine how to utilize the health benefits of both microalgae.