Conserved Signature Indels (CSIs) in protein sequences, which are specific for species from different genera demonstrate strong predictive potential of being found in other members of these genera. For several recently described Pseudomonadaceae genera (viz Aquipseudomonas, Atopomonas, Caenipseudomonas, Chryseomonas Ectopseudomonas, Geopseudomonas, Halopseudomonas, Metapseudomonas, Phytopseudomonas, Serpens, Stutzerimonas, Thiopseudomonas, and Zestomonas), multiple taxon-specific CSIs have been identified. This study examines the potential applications of these CSIs for identifying unclassified Pseudomonas spp. (strains) related to these genera. This was done using the AppIndels.com server, which uses information for the known taxon-specific CSIs in a genome sequence for predicting its taxonomic affiliation. For these studies, sequence information for different CSIs specific for the Pseudomonadaceae genera, and specific for P. aeruginosa and P. paraeruginosa, were added to the server’s database. The server was then used to analyze the genomes of 1972 Pseudomonas spp. (strains/isolates) of unknown taxonomic affiliation. Based upon the analyses conducted by the AppIndels server, which determined the presence of significant number of taxonspecific CSIs in the analyzed genome, the server predicted that 299 of the analyzed genomes corresponded to the following clades/genera: Pseudomonas sensu stricto clade (46 strains), Ectopseudomonas (46 strains), Chryseomonas (32 strains), Stutzerimonas (31 strains), Metapseudomonas (22 strains), Aquipseudomonas (21 strains), Phytopseudomonas (17 strains), Halopseudomonas (9 strains), Geopseudomonas (4 strains), Thiopseudomonas (3 strains), Serpens (2 strains), Caenipseudomonas (1 strain) and Zestomonas (1 strain). Additionally, 64 examined Pseudomonas spp. genomes were identified as P. aeruginosa. Phylogenetic studies performed here show that the taxonomic predictions made by the server were 100% accurate. Thus, based upon genome sequence information, the identified taxonspecific CSIs provide a novel and useful means for identifying other species/strains affiliated with the specific genera. The results of phylogenetic studies also suggest that many unclassified Pseudomonas strains whose taxonomic affiliations was predicted would likely constitute novel species in the indicated genera.