The Javan gibbon, Hylobates moloch, is an endangered gibbon species restricted to the forest remnants of western and central Java, Indonesia, and one of the rarest of the Hylobatidae family. Hylobatids consist of four genera (Holoock, Hylobates, Symphalangus, and Nomascus) that are characterized by different numbers of chromosomes, ranging from 38 to 52. The underlying cause of this karyotype plasticity is not entirely understood, at least in part, due to the limited availability of genomic data. Here we present the first scaffold-level assembly for the Hylobates moloch using a combination of whole genome Illumina short-reads, 10X Chromium linked reads, PacBio, and Oxford Nanopore long reads and proximity ligation data. This Hylobates genome represents a valuable new resource for comparative genomics studies in primates.