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Multilocus sequence analysis (MLSA) and multilocus sequence typing (MLST) are nowa‐ days considered as gold standards in the study of microbial systematic, being both tech‐ niques based on the interpretation of the sequences of several housekeeping genes. In this context, the sequences can be analyzed from different points of view. On the one hand, the phylogeny of the bacterial species can be estimated using the MLSA approach and on the other hand, the structure of the population can be inferred by means of MLST. Moreover, most species display some degree of population structure that can be inter‐ preted in geographic and chronological contexts, that is, phylogeographic studies. In this review, the phylogeny and population structure of two important fish and shell‐ fish pathogens, Yersinia ruckeri and Vibrio tapetis, exhibiting very different evolutive pat‐ terns will be analyzed. In both cases, the species form robust and monophyletic groups from a phylogenetic point of view. Regarding to the population structure, very different results were found. While Y. ruckeri follows an epidemic model of clonal expansion with well‐adapted clones that explode to be widely distributed, V. tapetis appears to have a mixed structure in where the paradox of clonality and high level of variability coexist. Furthermore, phylogeographical studies provided the evolutionary and geographical context for the species, allowing the determination of historical and spatial influences on the diversification of both species.

From the Gene Sequence to the Phylogeography through the Population Structure: The Cases of Yersinia ruckeri and Vibrio tapetis