<p>At present the development and application of antibiotics has shown a downward trend. This is attributed to the overuse of antibiotics leading to an increase in multidrug-resistant bacterial strains. Therefore, it is important to identify alternative antibacterial substances that can help avoid the development of resistance. Antimicrobial peptides (AMPs) are widely found in nature and are not susceptible to drug resistance, making them candidates as an alternative to traditional antibiotics. Microalgae are an important source of AMPs. <i>Spirulina</i> contains natural AMPs that play an important role in aquatic ecosystems. However, due to the rapid development of genetic engineering technology, other microalgae have shown significant potential for the heterologous expression of AMPs and have become a research hotspot. Among the three commonly used heterogeneous production systems (bacteria, fungi, and microalgae), microalgae have shown the main advantages of both prokaryotic and eukaryotic production systems and are expected to become a substitute production platform of AMPs. It is reported that appropriate genetic elements can be selected to express a variety of AMPs with their antibacterial activities verified in the nuclei or chloroplasts of several microalgal taxa. Due to its effective prevention of gene silencing, chloroplast expression is more advantageous than nuclear expression. In this review, we provide a brief overview of the classification of AMPs based on their secondary structure, their mechanism of action, and the natural AMPs found in microalgae. We have focused on the research progress in utilizing microalgae as a production platform for AMPs and on the application of AMPs produced by microalgae.</p>