Mesophotic coral ecosystems (MCEs: ~30 to 100+ m depth) may be older and more stable than shallow coral ecosystems that are more prone to disturbances in both the long term (glacial sea level cycles) and short term (heavy weather and anthropogenic activities). Here, we assess the phylogeography of two MCE fishes, the soldierfish Myripristis chryseres (N = 85) and the squirrelfish Neoniphon aurolineatus (N = 74), with mtDNA cytochrome oxidase C subunit I. Our goal is to resolve population genetic diversity across the Central and West Pacific and compare these patterns to three shallow-reef species in the same taxonomic family (Holocentridae). Significant population structure (ΦST = 0.148, p = 0.01) was observed in N. aurolineatus, while no structure was detected in M. chryseres (ΦST = −0.031, p = 0.83), a finding that matches the shallow-water congener M. berndti (ΦST = −0.007, p = 0.63) across the same range. Nucleotide diversity in the MCE fishes was low (π = 0.0024–0.0028) compared to shallow counterparts (π = 0.003–0.006). Coalescence times calculated for M. chryseres (~272,000 years) and N. aurolineatus (~284,000 years) are more recent or comparable to the shallow-water holocentrids (~220,000–916,000 years). We conclude that the shallow genetic coalescence characteristic of shallow-water marine fishes cannot be attributed to frequent disturbance. We see no evidence from holocentrid species that MCEs are older or more stable habitats.