In 2022, an outbreak of H5N1 highly pathogenic avian influenza (HPAI) killed 60% of the largest breeding colony of Dalmatian pelican (DP) in the world, at Mikri Prespa Lake (Greece), prompting a multidisciplinary study on HPAI and other pathogens. This study determines the antimicrobial resistance rates of cloacal enterococci and Escherichia coli in DPs. Fifty-two blood and cloacal swab samples were collected from 31 nestlings (20 DP/11 great white pelicans) hatched after the H5N1 outbreak at the Prespa colony and 21 subadult/adult DPs captured at a spring migration stopover. Swabs were inoculated in non-selective and chromogenic selective media. Identification was performed by MALDI-TOF, and antimicrobial susceptibility was tested. The genetic content was characterized by PCR-sequencing and the clonality of extended-spectrum-betalactamase (ESBL)-producing-E. coli isolates by Multi-Locus-Sequence-Typing. Twenty-eight non-repetitive E. coli and 45 enterococci isolates were recovered in non-selective media; most of them were susceptible to all antibiotics tested (85.7% E. coli/91.1% enterococci). Three of 52 samples (6%, all adults) contained ESBL-E. coli isolates (detected in chromogenic ESBL plates), all carrying the bla_CTX-M-15 gene and belonging to the lineage ST69. Despite the susceptibility of most fecal E. coli and enterococci isolates to all antibiotics tested, the identification of E. coli of lineage ST69 carrying blaCTX-M-15 is of concern. This high-risk clone needs further investigation to elucidate its primary sources and address the growing threat of antimicrobial resistance from an integrated 'One Health' perspective. Furthermore, it is imperative to further study the potential impacts of ESBL-E. coli on the endangered DP.