Botrytis cinerea stands out for having a wide host range and is qualified as generalist. Nevertheless, recent studies suggest that it actually corresponds to co-existing populations that show a certain level of host specialization, as described for the French populations T and G1, specialized on tomato and grapevine, respectively (Mercier et al., 2019, Env. Microbiol. 21, 4808–21; Mercier et al., 2021 Phytopathology, 111,2355-66). What are the molecular determinants responsible for such host-specialization? Previous Illumina sequencing data revealed genes under positive selection encoding cellulases, pectinases and enzymes involved in the oxidative stress response suggesting that these activities may contribute to the specialization on tomato. Here, using PacBio sequencing, we produced complete assemblies and annotation of the genomes of strains Sl3 and Vv3 that represent the T and G1 populations in order to identify all possible genomic correlates of hostspecialization. Both assemblies revealed 16 core chromosomes that were highly syntenic with those of the reference strain B05.10. The main sources of variation in gene content were the subtelomeric regions and the accessory chromosomes (ACs), especially the AC BCIN19 of Vv3 that was absent in Sl3 and B05.10. The repertoires and density of transposable elements (TEs) were clearly different between the genomes of Sl3 and Vv3 with a larger number of subfamilies (26) and a greater genome coverage in Vv3 (7.7%) than in Sl3 (14 subfamilies, 4.5% coverage). An Helitron-like TE was found in almost all subtelomeric regions of the Vv3 genome, in particular in the flanking regions of a highly duplicated gene encoding a Telomere-Linked Helicase, while both features were absent from the Sl3 and B05.10 genomes. Different retrotransposons in the Sl3 and the Vv3 strains resulted in the synthesis of distinct sets of small RNAs. Finally, extending the study to additional strains indicated that the AC BCIN19 and the small RNAs producing TE Copia_4 and Gypsy_7 are common features of the G1 population that are scarcely if ever found in strains isolated from other populations. This research reveals that ACs, TEs and their derived small RNAs differ between populations of B. cinerea specialized on different hosts and paves the way for further studies aiming at investigating the molecular mechanisms underpinning host specialization in a polyphagous pathogen (Simon et al., BioRxiv, https://doi.org/10.1101/2022.03.07.483234).