To test the level of compatibility, it is necessary to test the effectiveness of the type of Arbuscular Mycorrhizal Fungi (AMF) with shallots on the greenhouse scale, which can be seen from the growth and the results as well as answering the question of the compatibility level of isolate / type AMF to improve the quality of shallots based on essential oil content produced. The objectives of the study were (1) to find compatible indigenous AMF type for shallots on growth and yield, (2) to see the effect of indigenous AMF on shallots bulbs quality from the essential oil content. The potted study was prepared using Completely Randomized Design, with one factor of mycorrhizal (M) with 6 type (Scutelospora sp1, Glomus sp1, Glomus sp2, Glomus sp3, Gigaspora sp1,Glomus sp4) and 1 treatment without inoculation of AMF. The similarity of variance between treatments was tested with Duncan\'s Multiple Range Test (DMRT) at a 5% significance level. The results of the study showed that (1) All types of AMF tested were able to increase colonization, plant height and shallots yield, but were not significantly different to the number of tillers and number of leaves, (2) Inoculation of all types of AMF can increase the essential oil content of shallots bulbs. Conclution:There were differences in the effectiveness between the six isolates of AMF on root colonization, plant height, yield and essential oil content of shallots. Glomus sp1, Glomus sp2 and Glomus sp3 were potential isolates to be applied to shallots cultivation.