Plants in terrestrial and aquatic environments contain a diverse microbiome. Yet, the chloroplast and mitochondria organelles of the plant eukaryotic cell originate from free‐living cyanobacteria and Rickettsiales. This represents a challenge for sequencing the plant microbiome with universal primers, as ~99% of 16S rRNA sequences may consist of chloroplast and mitochondrial sequences. Peptide nucleic acid clamps offer a potential solution by blocking amplification of host‐associated sequences. We assessed the efficacy of chloroplast and mitochondria‐blocking clamps against a range of microbial taxa from soil, freshwater and marine environments. While we found that the mitochondrial blocking clamps appear to be a robust method for assessing animal‐associated microbiota, Proteobacterial 16S rRNA binds to the chloroplast‐blocking clamp, resulting in a strong sequencing bias against this group. We attribute this bias to a conserved 14‐bp sequence in the Proteobacteria that matches the 17‐bp chloroplast‐blocking clamp sequence. By scanning the Greengenes database, we provide a reference list of nearly 1500 taxa that contain this 14‐bp sequence, including 48 families such as the Rhodobacteraceae, Phyllobacteriaceae, Rhizobiaceae, Kiloniellaceae and Caulobacteraceae. To determine where these taxa are found in nature, we mapped this taxa reference list against the Earth Microbiome Project database. These taxa are abundant in a variety of environments, particularly aquatic and semiaquatic freshwater and marine habitats. To facilitate informed decisions on effective use of organelle‐blocking clamps, we provide a searchable database of microbial taxa in the Greengenes and Silva databases matching various n‐mer oligonucleotides of each PNA sequence.