The influence of geomagnetic field on various biological processes is certainly an interesting research field, and more work is beingperformed across the globe. However, the impact of varying magnetic flux density on plant circadian rhythms has not yet beencompletely investigated. Different researchers have mostly focused their attention on the molecular workings of circadian rhythms invarious plant systems and the circadian architecture of transcriptomes under varying conditions. The present investigation evaluatedthe influence of variable geomagnetic field on the expression of genes that are under the control of circadian rhythm, and checkedwhether the expression pattern of these genes with respect to time (circadian nature) under different magnetic flux density changesor not in Arabidopsis seedlings. This study examined the impact of varying magnetic flux densities on the mRNA expression levels ofsix genes in Arabidopsis thaliana during the final 33 hours of their total 120 hour growth period. A. thaliana seedlings were subjectedto four distinct magnetic flux densities (0, 25, 50, and 90 μT), and the abundance of transcripts for chlorophyll a/b binding protein 4,the large subunit of RuBisCO, rubisco activase, chalcone synthase, porphobilinogen synthase, and phytoene dehydrogenase genes wasexamined. While the present study’s findings lend credence to the idea that the aforementioned genes are differentially expressed inresponse to changes in magnetic flux density, it also proved that the circadian nature of these genes was largely unaffected, with theirexpression pattern remaining largely unaltered regardless of the strength of the magnetic field.