Fowl adenoviruses (FAdVs) are grouped into five different species: Fowl adenovirus A through Fowl adenovirus E (FAdV-A to FAdV-E), and so far, complete nucleotide sequences are only available for the genomes of FAdV-A, FAdV-C, FAdV-D and FAdV-E members. The aim of this study was to sequence and analyze the complete genome of the reference strain representing FAdV-B (FAdV-5, strain 340). By applying Next Generation Sequencing, the genome was found to be 45,781 bp long with 56.5% G+C content, and being very similar to the other FAdV strains. Genome organization and phylogenetic analyses confirmed the present division of the genus Aviadenovirus into species and the closer genetic relationship between FAdV-D and FAdV-E. In the left end region of the genome, homologues to the first predicted genes (ORF0-ORF12) described for FAdV-C (strain KR5) were present in the genome of strain 340, but ORFs 14B and 14C were absent. The central part of the strain 340 genome (IVa2-pVIII) showed an organization identical to that of other adenoviruses (but lacking the gene of protein V, which occurs only in mastadenoviruses). Just one fiber gene was identified. The right end region of the genome showed more heterogeneity. The predicted gene content within this region varies among aviadenoviruses, while the gene order and orientation of shared ORFs are conserved between different aviadenoviruses. With the completion of full genomes from all fowl adenovirus species, additional insights into the evolution of genus Aviadenovirus were obtained.