The skeleton of reef-building coral harbors diverse microbial communities that could compensate for metabolic deficiencies caused by the loss of algal endosymbionts, i.e., coral bleaching. However, it is unknown to what extent endolith taxonomic diversity and functional potential might contribute to thermal resilience. Here we exposed Goniastrea edwardsi and Porites lutea, two common reef‐building corals from the central Red Sea to a 17-day long heat stress. Using hyperspectral imaging, marker gene/metagenomic sequencing, and NanoSIMS, we characterized their endolithic microbiomes together with ¹⁵N and ¹³C assimilation of two skeletal compartments: the endolithic band directly below the coral tissue and the deep skeleton. The bleaching-resistant G. edwardsi was associated with endolithic microbiomes of greater functional diversity and redundancy that exhibited lower N and C assimilation than endoliths in the bleaching-sensitive P. lutea. We propose that the lower endolithic primary productivity in G. edwardsi can be attributed to the dominance of chemolithotrophs. Lower primary production within the skeleton may prevent unbalanced nutrient fluxes to coral tissues under heat stress, thereby preserving nutrient-limiting conditions characteristic of a stable coral-algal symbiosis. Our findings link coral endolithic microbiome structure and function to bleaching susceptibility, providing new avenues for understanding and eventually mitigating reef loss.

造礁珊瑚的骨架包含多种微生物群落，这些微生物群落可以补偿由藻类内共生体丧失（即珊瑚白化）引起的代谢缺陷。然而，尚不清楚内层生物分类学多样性和功能潜力在多大程度上有助于热恢复。在这里，我们将红海中部的两种常见造礁珊瑚Goniastrea edwardsi和Porites lutea暴露于长达 17 天的热应激条件下。使用高光谱成像、标记基因/宏基因组测序和 NanoSIMS，我们表征了它们的内生微生物组以及¹⁵ N 和¹³C 两个骨骼隔间的同化：珊瑚组织正下方的内石带和深层骨骼。抗漂白的G. edwardsi与具有更大功能多样性和冗余的内生微生物组相关，与漂白敏感的P. lutea中的内生微生物相比，它们表现出更低的 N 和 C 同化作用。我们建议G中较低的内生初级生产力。爱德华西可归因于化学无机营养生物的优势。骨骼内较低的初级生产可以防止在热应激下珊瑚组织的营养通量不平衡，从而保持稳定的珊瑚 - 藻类共生的营养限制条件。我们的研究结果将珊瑚内生微生物组的结构和功能与漂白敏感性联系起来，为理解并最终减轻珊瑚礁损失提供了新途径。