Metabolic fingerprinting can elucidate rearrangements of metabolic networks in organisms exposed to various environmental conditions. Maintenance of organismal performance occurs by alterations in metabolic fluxes and pathways, resulting in habitat-specific metabolic signatures. Several insects of sub-Antarctic Islands, including the wingless flies Anatalanta aptera and Calycopteryx moseleyi, are exposed to saline organic matter accumulated along littoral margins. However, C. moseleyi has long been considered restricted to a habitat of lower salinity, the Kerguelen cabbage. High C. moseleyi densities identified in saline decaying seaweeds are intriguing, and may involve osmoregulatory adjustments including accumulation of osmoprotectants. In the present work, we examined quantitative metabotypes (metabolic phenotypes) among wild C. moseleyi individuals from seaweeds versus non-saline Kerguelen cabbages. They were compared to metabotypes from wild A. aptera, a common fly on seaweed. Statistical procedures designed to magnify between-class differences failed to clearly separate C. moseleyi metabotypes from cabbage and seaweed, despite contrasted morphotypes, diets, and salinities. A. aptera exhibited higher glycerol, inositol, trehalose, and other osmoprotectants concentrations that may enhance its performance under saline environments. Seaweed may represent a secondary niche in C. moseleyi, promoted by the marked reduction in Kerguelen cabbage frequency subsequent to climate change, and herbivorous pressures caused by rabbit invasion.