To evaluate the expression patterns of genes involved in iron and oxygen metabolism during magnetosome formation, the profiles of 13 key genes in Magnetospirillum gryphiswaldense MSR-1 cells cultured under high-iron vs. low-iron conditions were examined. Cell growth rates did not differ between the two conditions. Only the high-iron cells produced magnetosomes. Transmission electron microscopy observations revealed that magnetosome formation began at 6 h and crystal maturation occurred from 10 to 18 h. Real-time polymerase chain reaction analysis showed that expression of these genes increased during cell growth and magnetosome synthesis, particularly for ferric reductase gene (fer6) and ferrous transport system-related genes feoAB1, feoAB2, sodB, and katG. The low-iron cells showed increased expression of feoAB1 and feoB2 from 12 to 18 h but no clear expression changes for the other genes. Expression patterns of the genes were divided by hierarchical clustering into four clusters for the high-iron cells and three clusters for the low-iron cells. Each cluster included both iron and oxygen metabolism genes showing similar expression patterns. The findings indicate the coordination and co-dependence of iron and oxygen metabolism gene activity to achieve a balance during the biomineralization process. Future transcriptome analysis will help elucidate the mechanism of biomineralization in MSR-1 magnetosome formation.