In this paper, we discuss the use of a direct thermal desorption (DTD) interface as an alternative to Curie-point flash pyrolysis system as an inlet technique in gas chromatography–combustion isotope-ratio mass spectrometry (GC/C-IRMS) analysis of whole/intact phytoplankton and zooplankton specimens. The DTD in combination with a combipal auto-injector is programmed to perform the injection, evaporation of solvents, transport of capped programmed-temperature vaporizer (PTV) liners to the PTV injector and chemical derivatisation (thermally assisted hydrolysis/methylation; THM) such that a profile of a cellular fatty acids is obtained. Flow-cytometric sorted microalgae and handpicked zooplankton are used as samples with trimethylsulfonium hydroxide (TMSH) as methylating reagent. A major advantage of this novel approach over the Curie-point technique is the automation of the total procedure, which allows unattended analysis of large sample series. The profiles and δ13C carbon isotopic signatures of the fatty acid methyl esters (FAMEs) produced are very similar to those obtained using the Curie-point flash pyrolysis method. It is shown that algal samples must be kept no longer than 48 h in the DTD sample tray prior to the THM-analysis in order to maintain the integrity of their FAME profile.