- The relationships between pigment (carotenoid and chlorophyll) content with accumulation of total fatty acids (TFA) and arachidonic acid (AA) were studied in the green microalga Parietochloris incisa (Trebouxiophyceae, Chlorophyta) grown under different PFDs (35, 200, and 400μmol photons m−2 s−1) and nitrogen availabilities. The growth of P. incisa under higher light and nitrogen deficiency was accompanied by accumulation of FA, an increase in carotenoid and a decline in chlorophyll content. It was found that the carotenoid-to-chlorophyll ratio (but not the individual pigment content) correlates closely with the volumetric content of both TFA and AA. Analysis of scattering-compensated absorption spectra of P. incisa suspensions revealed their tight relationship in the blue-green range of the spectrum with the carotenoid-to-chlorophyll ratio, TFA, and AA content. These findings allowed the development of algorithms for the non-destructive assay of TFA and AA in cell suspensions in the ranges of 0.09–3.04 and 0.04–1.7μg mL−1, with accuracy of 0.06 and 0.01μg mL−1, respectively, via analytically measured carotenoid-to-chlorophyll ratio and using the ratio of absorption coefficients at 510 and 678nm, with accuracy of 0.07 and 0.02μg mL−1, respectively. The feasibility of obtaining essential spectral information concerning the physiological condition of P. incisa using a standard spectrophotometer is also shown.