Tomato plant cultivation is influenced by many factors, including the level of resistance of tomato plants to diseases. Several soil-borne diseases are detrimental to tomato plants, and especially when they attack nurseries. Meanwhile, nursery planting media is a part that needs to be considered so that the plants that are sought are healthy and provide maximum results. This study aims to determine the incidence of disease in tomato nurseries on different soil sources, determine the causes of diseases that attack tomato nurseries (Lycopersicum esculentum Mill.), and determine varieties that are resistant to disease attacks on tomato plants. This research was conducted at the green house, Agronomy Laboratory, Faculty of Agriculture, University of Mulawarman Samarinda and the Laboratory of Pest and Plant Disease Sciences, Faculty of Agriculture, Universitas Mulawarman, Samarinda. The treatment of soil, consisted of 5 levels. They are soil of ex-tomato plantation (t1), soil of ex-chilly plantation (t2), soil of ex-banana plantation (t3), soil of ex-rice plantation (t4) and soil of ex-alang-alang weed (t5). The variety treatment consisted of 2 levels, namely the Lentana variety (v1) and the Permata variety (v2). The design used in this study was a completely randomized design. The results showed that the lowest disease incidence was found in the ex-alang-alang soil; Most of the tomato nurseries were attacked by the fungus Fusarium sp; Lantana variety is more resistant compare to the Permata variety of tomato.