| Summary: | Caladiums are promising colorful foliage plants due to their unique leaf shapes and dazzling colors. Until now, over 2000 varieties of <i>Caladium</i> have been cultivated worldwide. The long-term natural variation and artificial selection have enriched the germplasm resources of <i>Caladium</i> in the market, yet have blurred its genetic background. In this study, 16 informative EST-SSR markers were used to screen 144 <i>Caladium</i> accessions, indicating that 16 EST-SSRs could distinguish all genotypes with a minimum cumulative identity probability (PI) of 2.0 2 × 10<sup>−15</sup>. Using the simulated annealing method, the richest genetic information was acquired at the same compression ratio. A final core of 44 accessions was selected, comprising 30.6% of the individuals and retraining more than 95% of the total genetic information. No significant differences were observed in allele frequency distributions or genetic diversity parameters between the core collection and the entire population. Cluster analysis roughly divided the core collections into four populations, where 66.7% of the private alleles were detected in Pop2. Finally, DNA molecular fingerprints of 44 core accessions were established, including barcodes and quick response (QR) code molecular identities (ID). The results will lay a theoretical foundation for identifying, preserving, and utilizing <i>Caladium</i> germplasm resources.
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