This study established polymerase chain reaction (PCR) conditions for in vitro amplification of eukaryotic small subunit ribosomal (16S-like) rRNA genes. The method was applied to amplify coding regions from algae, fungi, and protozoa using nanogram quantities of genomic DNA or recombinant plasmids containing rDNA genes. Oligodeoxynucleotides complementary to conserved regions at the 5' and 3' termini of eukaryotic 16S-like rRNAs were used to prime DNA synthesis in repetitive cycles. The fidelity of the amplification products was evaluated by comparing them with previously reported rRNA sequences or through primer extension analyses. The results showed that fewer than one error per 2000 positions occurred in the amplified rRNA coding region sequences. The primary structure of the 16S-like rRNA from the marine diatom, Skeletonema costatum, was inferred from the sequence of its in vitro amplified coding region. The study also discussed the potential impact of this technology on the analysis of natural microbial populations and the phylogenetic status of S. costatum, which was found to be most similar to those of A. bisexualis and O. danica.This study established polymerase chain reaction (PCR) conditions for in vitro amplification of eukaryotic small subunit ribosomal (16S-like) rRNA genes. The method was applied to amplify coding regions from algae, fungi, and protozoa using nanogram quantities of genomic DNA or recombinant plasmids containing rDNA genes. Oligodeoxynucleotides complementary to conserved regions at the 5' and 3' termini of eukaryotic 16S-like rRNAs were used to prime DNA synthesis in repetitive cycles. The fidelity of the amplification products was evaluated by comparing them with previously reported rRNA sequences or through primer extension analyses. The results showed that fewer than one error per 2000 positions occurred in the amplified rRNA coding region sequences. The primary structure of the 16S-like rRNA from the marine diatom, Skeletonema costatum, was inferred from the sequence of its in vitro amplified coding region. The study also discussed the potential impact of this technology on the analysis of natural microbial populations and the phylogenetic status of S. costatum, which was found to be most similar to those of A. bisexualis and O. danica.