OBJECTIVE To compare the halometabolite producing capability between actinomycetes of earth origin and marine origin, based on genetic screening of the 1,5-dihydroflavin adenine dinucleotide (FADH2-dependent) halogenase gene. METHODS We used 141 actinomycete isolates that were dereplicated by phenotype, 70 of earth origin and 71 of marine origin, and obtained halogenase gene fragments from them by PCR screening. We then sequenced the PCR products and analyzed corresponding amino acid sequences phylogenetically. We made further comparison of the halogenase sequences between actinomycetes of different origins, and between marine-origin streptomycetes and marine-origin Micromonospora isolates. In addition, we detected polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes by PCR in the halogenase gene-positive isolates. RESULTS We observed higher occurrence of the halogenase gene in marine-origin actinomycetes (36.6%) than in earth-origin actinomycetes (14.3%), and in marine-origin streptomycetes (69.0%) than in marine-origin Micromonospora isolates (14.3%). Most (86.1%) of the halogenase gene-positive isolates contained PKS and/or NRPS genes. Moreover, the halogenase sequences of marine-origin isolates differed largely from the known ones, and clustered into a couple of distinct clades in the phylogenetic tree. In addition, we found greater diversity of the halogenase genes in marine-origin Micromonospora isolates than in marine-origin streptomycetes. CONCLUSION Based on the results of this study, we propose that actinomycetes, especially streptomycetes, from marine habitat could serve as a good source for new bioactive halometabolite discovery in the future.