Here we report the complete genome sequence of Aquimarina sp. strain EL43 isolated from Eunicella labiata off the coast of Algarve, South Portugal. The genome was sequenced using the 10-hour movie time on a PacBio Sequel (Pacific Biosciences) apparatus and assembled De Novo into two contigs with an N50 contig length of 6,121,210 bp. Genome assembly was accomplished using the SMRT Analysis Hierarchical Genome Assembly Process (HGAP; SMRT Link 9.0.0). This assembly submitted herewith is an alternative to the earlier assembly submitted for the same strain under the assembly accession number GCA_015752065.1 (sample accession: SAMN16784347; study accession: PRJNA676412), which was based on Illumina sequencing technology.