Cyanobacteria are photosynthetic microorganisms that can utilise white, far-red or UV light. The organisms adapt their cellular metabolism to their environment by regulating their genetic expression to accumulate or reduce metabolites such as valuable polyunsaturated fatty acids. The production of high-value metabolites whilst using light and CO2 to grow make these organisms a successful candidate within the biotechnological industry. Far-red light is known to influence cyanobacteria, especially their photosynthetic apparatus. Thylakoid membranes are known to be altered by far-red light photoacclimation (FaRLiP). However, the role of fatty acid synthesis and desaturation during FarLip is little studied. This study examines the gene expression of 33 fatty acid-related genes when the cyanobacterium Chlorogloeopsis fritschii PCC 6912 is grown under far-red light compared to white light using RNA-seq data from the NCBI database. The transcriptomic analysis, encompassing a bioinformatic pipeline to process and quantify transcripts, found that only two genes of the 33 examined genes were differentially expressed. The two genes were down-regulated and encoded for a fatty acid desaturase (fad) and a pfaD/polyketide biosynthesis protein. The results suggest that fatty acid desaturation decreases in favour of saturated fatty acids. Furthermore, the identification of a pfa gene cluster may highlight a secondary path of polyunsaturated fatty acids within heterocyst cyanobacteria. This study also highlights the need for greater biological replicates within RNA-seq experiments and increased completeness in genome annotations in biotechnological databases.