This chapter discusses the isolation of endosymbiotic microorganisms such as bacteria, actinobacteria, and fungi from green algae. Several methods for collecting and sterilizing algal samples are discussed, ensuring that the isolated microorganisms are truly endosymbiotic. Each species of endosymbionts is cultured on a different medium like nutrient agar (NA) for bacteria, actinomycete isolation agar (AIA) and International Streptomyces Project Medium (ISP-2) for actinobacteria, and potato dextrose agar (PDA) with streptomycin for fungi. Successful endosymbiont isolation requires adequate sample handling, sterilization techniques, and appropriate conditions to encourage the growth of desired microorganisms while inhibiting contaminants.