The high cost and environmental impact of traditional microalgal harvesting methods limit commercialization of microalgal biomass. Fungal bioflocculation of microalgae is a promising low-cost, eco-friendly method but the range of fungal and microalgal species tested to date is narrow. Here, eight non-pathogenic, filamentous fungi were screened for their ability to self-pelletize and flocculate Euglena gracilis (ca.50 µm motile microalga) in suspension. Self-pelletization was tested under various rotational speeds, and species which formed pellets (Ø > 0.5 cm) were selected for harvesting tests. Filaments of each species were combined with E. gracilis at various ratios based on dry weight. Harvesting efficiency was determined by measuring the change in cell counts over time, and settling of the flocs was evaluated by batch settling tests. Three fungal species, Ganoderma lucidum, Pleurotus ostreatus, and Penicillium restrictum, were able to reliably flocculate and harvest 62–75% of the microalgae while leaving it unharmed. The results demonstrated that self-pelletization, harvesting, and settling were dependent on the fungal species. The fungi to algae ratio also had significant but contrasting effects on harvesting and settling. In balancing the needs to both harvest and settle the biomass, the optimal fungi to algae ratio was 1:2. The application of fungal filaments to microalgae in suspension produced readily settling flocs and was less time-consuming than other commonly used methods. This method is especially attractive for harvesting microalgal biomass for low-value products where speed, low cost, and cell integrity is vital.