Copepods are one of the most abundant invertebrate groups in the seas and oceans and are a significant food source for marine animals. Copepods are also particularly sensitive to elevated temperatures. However, it is relatively unknown the role of the internal microbiome in shaping copepod susceptibility to warming. We addressed this fundamental knowledge gap by assessing key life history traits (survival, development, reproduction), and changes in the internal microbiome in the tropical calanoid copepod Acartia sp. in response to warming (26, 30, and 34°C). Copepod microbiomes were analyzed using high throughput DNA sequencing of V1–V9 of 16S rRNA hypervariable regions. Copepod performance was better at 30°C than at 26°C as indicated by higher survival, faster growth rate and development, and higher fecundity. However, these parameters strongly decreased at 34°C. We recorded 1,262,987 amplicon sequence reads, corresponding to 392 total operational taxonomic units at 97% similarity. The copepod microbiomes contained Proteobacteria, Bacteroidetes, Planctomycetes, Actinobacteria, and Acidobacteria. Importantly, the internal microbiota biodiversity was strongly reduced at higher temperatures. The highest number of OTUs was obtained at 26°C (126/392 OTUs), and the lowest was at 34°C (31/392 OTUs). The thermophilic Proteobacteria was dominant under elevated temperatures (30°C and 34°C). At 34°C, Vibrio accounted for 70% of bacterial species in copepods. The reduced OTUs number with an increased relative abundance of Vibrio seemed to be related to the reduced copepod growth and survival. Profiling the functional role of all internal bacterial groups as a function of the temperature change will fundamentally advance our mechanistic understanding of the performance of tropical copepods and, more generally, marine invertebrates to a warming climate.