Carbon nanotube (CNT)-based materials have attracted tremendous interest for their high performance in oil separation. However, the preparation of CNT based materials always require harmful and expensive chemicals. Here, a biological assembly route was applied to assemble CNTs onto a fungal hyphae (FH) to produce FH/CNTs composites, followed by pyrolysis to obtain a hydrophobic CNT based aerogel for oil separation, which is a more environmentally friendly process. The as-prepared FH/CNTs-800 aerogel (pyrolyzed at 800 °C) showed hydrophobicity with a water contact angle of 143° and high specific surface area (1041.2 m2 g-1). The oil absorption results showed that the as-prepared FH/CNTs aerogels could absorb a wide range of oils with high absorption capacities ranging from 48 to 138 times their own weight. Furthermore, the oil-loaded aerogel was recycled through burning with little reduction in the oil absorption capacity. In addition, FH/CNTs-800 provided a high specific capacitance of 232 F g-1 at 1 A g-1 and maintained a capacity retention of 70.62% at 20 A g-1. Therefore, this study offers a simple, low-cost and environmentally friendly bioassembly route for large-scale assembly of CNTs into macroscopic 3D hydrophobic aerogels for highly efficient water-oil separation.