Nostoxanthin, a yellow pigment, belongs to the xanthophyll group of carotenoids found in various species of bacteria and cyanobacteria. Several species of
Sphingomonas
can produce appropriate carotenoids for survive in various environments. This comprise nostoxanthin, a significant carotenoid. The study isolated the
Sphingomonas
species strain COS14-R2 from the
Cosmos bipinnatus
and identified it through the whole-genome sequence. The strain consists of a circular chromosome with a length of 3,677,457 base pairs.s ecThe genome consists of three carotenoid biosynthesis genes, specifically
crtB
(phytoene synthase),
crtI
(phytoene desaturase), and
crtY
(Lycopene beta-cyclase), which are involved in the synthesis of nostoxanthin. The strain has a circular, undulated colony morphology with a deep yellow color. It demonstrates optimal growth in liquid media at 25 to 35 °C and exhibits a high tolerance for pH levels between 5 and 11 and requires adequate quantities of carbon and nitrogen. We observed the highest concentration of nostoxanthin was recorded at 35 °C, pH of 7.5, glucose concentration of 40 g L
−1
, and a yeast extract concentration of 5 g L
−1
during dark incubation. The fed-batch fermentation process produced nostoxanthin at a concentration of 217.22 ± 9.60 mg L
−1
, with a selectivity of 72.32% and a productivity of 2.59 g/L/h. The dry biomass extract was purified using column chromatography. The LC–MS/MS analysis of the purified fraction indicated that the molecular weight of nostoxanthin is 600.5098 m/z. The DPPH assay result of 75.5 ± 0.33% indicates nostoxanthin is highly effective in scavenging free radicals.