Phosphopantetheinyl transferases (PPTases) play essential role in the biosynthesis of fatty acids, polyketides, and nonribosomal peptides. PPTases phosphopantetheinylate carrier proteins in polyketide synthases (PKSs), fatty acid synthases (FASs) and nonribosomal peptide synthetases (NRPSs). In this review, we discuss current studies on the substrate specificities of PPTases to carrier proteins in Streptomyces. The substrates of type Ⅲ PPTases are acyl carrier proteins (ACPs) which locate within the same PKSs. The favorite substrates of typeⅠ PPTases are ACPs in typeⅡ FASs and typeⅡ PKSs. The favorite substrates of typeⅡ PPTases are ACPs in typeⅠ PKSs and peptidyl carrier proteins (PCPs) in NRPSs. The favorite substrates of a typeⅠ/Ⅱ PPTase, whose encoding gene locates in a gene cluster, are ACPs/PCPs whose encoding genes locate in the same gene cluster.