'Candidatus Phytoplasma pyri', the pathogen associated with pear decline, affects pear trees across both the old and new worlds. However, research on this phytoplasma has been limited by the lack of genomic data. This study presents the first draft genome of 'Ca. P. pyri' using a strain from Chile, with its genomic features analyzed in comparison to the closely related 'Ca. Phytoplasma' species, 'Ca. P. mali' and 'Ca. P. prunorum'. The draft genome spans 456,478 bp with a GC content of 20.4%. Key genes possibly associated with pathogenicity and potential pathogenic effectors were identified, and they are notably lacking orthologs of known effectors. A single potential mobile unit similar to that of 'Ca. P. mali' was identified. It is characterized by the absence of the transposase tra5 and the presence of the IS3 family transposase iSErh1. Multilocus sequence analysis (MLSA) of six genetic markers (16S rRNA gene, LSU36p, tuf, aceF, secA, and secY) from ten Chilean and ten Italian samples revealed high genetic uniformity among the Chilean strains, collected from five geographically distant orchards over a span of 13 months; by contrast, strains with greater diversity were detected among those from Italy collected from a few localities over approximately 30 years. These findings suggest limited evolutionary divergence of this phytoplasma in Chile. This study provides a foundational framework for investigations into the pathogenic mechanisms and evolutionary dynamics of 'Ca. P. pyri'.