An atomically thin MoSe2 layer has been synthesized on mica using molecular beam epitaxy (MBE). The polymorphous of the MoSe2 layer depends on the coverage and the growth temperature. At low coverages and low growth temperature, 1T-MoSe2 forms in addition to a comparable quantity of 2H-MoSe2. The metastable 1T-MoSe2 transfers gradually to the stable 2H-MoSe2 before the completion of the first monolayer. The current result sheds some light on the complexity of the nucleation and growth of transition metal dichalcogenide (TMDC) monolayers and implies a possible route for a phase selective synthesis using MBE.