Maize plants infected with Spiroplasma kunkelii show symptoms similar to that of plants in a magnesium-deficient soil, and it has been shown that the spiroplasma alters the plants' magnesium absorption. In the current study we compared changes associated to either spiroplasma infection, two soil magnesium levels and their combinations. Plant symptoms were recorded and correlated with transmission electron microscopy observations. Plants grown on a high magnesium treatment showed no macroscopical alterations nor organelle ultrastructural alterations, while plants on a low magnesium treatment showed macroscopical vein yellowing and, ultrastructurally, they had most chloroplasts and mitochondrial membranes altered. Infected plants on a low magnesium treatment had an ageing aspect, ultrastructurally showed chloroplasts and mitochondrial alterations similar to those non-infected and grown on a low magnesium treatment, and spiroplasma cells were found in phloem cells, but outside their cytoplasm. Infected plants on a high magnesium treatment showed similar symptoms and ultrastructural alterations as either non-infected plants on the low magnesium treatment or in infected plants on the low magnesium treatment, but differ from them in that the spiroplasma cells were located inside the cytoplasm. Results suggest that magnesium is involved in the plant-pathogen interaction.