The impact of microbiologically influenced corrosion on underwater archaeological sites has spurred recent advancements in research examining the link between microorganisms and historic preservation. Although the microbiomes of steel shipwreck sites have been the subject of DNA sequencing studies and other interdisciplinary investigations, aluminum submerged aircraft wrecks, a prominent symbol of World War II, have yet to be the focus of similar research. This article represents the initial attempt to fill this void by describing a biofilm collection method used to obtain samples for DNA sequencing from World War II aircraft sites off Hawaii. Rather than relying on proxies for microbial growth on wrecks or on destructive sampling, the focus is on a methodology that is productive but minimally intrusive. The protocols resulted in the successful collection of in situ biofilm samples from four submerged aircraft wrecks. The methodology was found to be affordable, time efficient, and reproducible, thus feasible for archaeological site management. The development of viable in situ collection methods for biofilm should aid efforts to empirically assess the relevancy of microbiologically influenced corrosion to submerged aircraft while enabling longitudinal studies of microorganisms that potentially affect site preservation.