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<i>Micromonospora</i> sp. AKA109 is a producer of akazaoxime and A-76356, whereas <i>Micromonospora</i> sp. AKA38 is that of levantilide C. We aimed to clarify their taxonomic positions and identify biosynthetic gene clusters (BGCs) of these compounds. In 16S rRNA gene and DNA gyrase subunit B gene (<i>gyrB</i>) sequence analyses, strains AKA109 and AKA38 were the most closely related to <i>Micromonospora humidisoli</i> MMS20-R2-29^T and <i>Micromonospora schwarzwaldensis</i> HKI0641^T, respectively. Although <i>Micromonospora</i> sp. AKA109 was identified as <i>M. humidisoli</i> by the <i>gyrB</i> sequence similarity and DNA–DNA relatedness based on whole genome sequences, <i>Micromonospora</i> sp. AKA38 was classified to a new genomospecies. <i>M. humidisoli</i> AKA109 harbored six type-I polyketide synthase (PKS), one type-II PKS, one type-III PKS, three non-ribosomal peptide synthetase (NRPS) and three hybrid PKS/NRPS gene clusters, among which the BGC of akazaoxime and A-76356 was identified. These gene clusters are conserved in <i>M. humidisoli</i> MMS20-R2-29^T<i>. Micromonospora</i> sp. AKA38 harbored two type-I PKS, one of which was responsible for levantilide C, one type-II PKS, one type-III PKS, two NRPS and five hybrid PKS/NRPS gene clusters. We predicted products derived from these gene clusters through bioinformatic analyses. Consequently, these two strains are revealed to be promising sources for diverse non-ribosomal peptide and polyketide compounds.