<p><i>Cronobacter</i> spp. are emerging opportunistic bacteria that are able to survive to diverse stresses. They infect mainly children through contaminated food. Despite the growing concern surrounding them, <i>Cronobacter malonaticus</i> (<i>C. malonaticus</i>) and <i>Cronobacter turicensis</i> (<i>C. turicensis</i>) remain understudied. This study aimed to characterize the genomic traits of <i>C. malonaticus</i> and <i>C. turicensis</i> isolated worldwide. A total of 104 <i>C. malonaticus</i> and 89 <i>C. turicensis</i> genomes from eight countries and diverse sources were screened for antimicrobial resistance and virulence genes, plasmids, and prophages. Genotyping was performed by Multi-Locus Sequence Typing (MLST), core-genome MLST, and Single-Nucleotide Polymorphism (SNP) clusters. Only six <i>C. malonaticus</i> genomes harbored resistance genes, while all <i>C. turicensis</i> genomes harbored the fosfomycin resistance gene <i>fos</i>. The IncFIB(pCTU1) and IncFIB(pCTU3) plasmid replicons and the prophage 118970_sal3 were the most frequent. Seventy-one virulence genes related to chemotaxis, flagella, hemolysins, intra-macrophage survival, outer membrane proteins, stress response and transcriptional regulation were found in all genomes. All molecular typing methods suggested a high intra-species genomic diversity, regardless of the isolation source or country. In conclusion, the high frequency of virulence genes in <i>C. malonaticus</i> and <i>C. turicensis</i> suggests their pathogenic potential and capacity to cause infection in humans, reinforcing the need to not underestimate the potential hazard of understudied <i>Cronobacter</i> species. The high genetic diversity, the presence of certain antimicrobial resistance genes, and the variety of plasmids and prophages reinforce the importance of monitoring <i>C. malonaticus</i> and <i>C. turicensis</i> worldwide by public health and food safety authorities.</p>