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The Mexican Central Pacific (MCP) region has discontinuous coral ecosystems with different protection and anthropogenic disturbance. Characterizing the bacterial assemblage associated with the sea urchin <i>Toxopneustes roseus</i> and its relationship with environmental variables will contribute to understanding the species’ physiology and ecology. We collected sea urchins from coral ecosystems at six sites in the MCP during the summer and winter for two consecutive years. The spatial scale represented the most important variation in the <i>T. roseus</i> bacteriome, particularly because of Isla Isabel National Park (PNII). Likewise, spatial differences correlated with habitat structure variables, mainly the sponge and live coral cover. The PNII exhibited highly diverse bacterial assemblages compared to other sites, characterized by families associated with diseases and environmental stress (<i>Saprospiraceae</i>, <i>Flammeovirgaceae</i>, and <i>Xanthobacteraceae</i>). The remaining five sites presented a constant spatiotemporal pattern, where the predominance of the <i>Campylobacteraceae</i> and <i>Helicobacteraceae</i> families was key to <i>T. roseus</i>’ holobiont. However, the dominance of certain bacterial families, such as <i>Enterobacteriaceae</i>, in the second analyzed year suggests that Punto B and Islas e islotes de Bahía Chamela Sanctuary were exposed to sewage contamination. Overall, our results improve the understanding of host-associated bacterial assemblages in specific time and space and their relationship with the environmental condition.