High-quality reference genomes permit deeper investigation into species’ evolution and provide insight into species conservation. Next-generation sequencing allows researchers to generate high-accuracy long-read genetic data in real-time from anywhere in the world, increasing accessibility to sequence data. The lava gull (Leucophaeus fuliginosus), an endemic bird of the Galapagos archipelago, is the world’s rarest gull with an estimated population of less than 400 pairs. Little research has been done on this species due to their small population size. We aim to sequence and assemble the lava gull reference genome for use in estimating genetic effective population size, studying population subdivision, identifying distinct conservation units, and providing other management information. We prepared a library from an adult female lava gull on San Cristobal island using Oxford Nanopore’s Ultra-Long DNA Sequencing Kit and sequenced using a PromethION 2 Solo. We generated 1.78 million reads, consisting of 29.4 gigabases at an estimated 22x coverage. A preliminary Flye assembly generated a total length of 1.34 Gb, with 1,363 contigs and an N50 of 37.1 million. The generation of the lava gull reference genome is an important step in determining this species’ conservation status and how best to focus management efforts.