Recent increases in hurricane activity along the Gulf of Mexico lend urgency to understanding storm impacts on beach mice (Peromyscus polionotus) that occupy dune systems along this coast in Florida and Alabama. We documented changes in occupancy patterns of the Santa Rosa beach mouse (P. p. leucocephalus) from Hurricane Ivan and examined predictors of habitat use before and after the hurricane. The hurricane removed 68% of frontal dune area occupied by beach mice and only 15% of scrub dune area. Occupancy of frontal dunes by beach mice dropped from 100% before to the hurricane to 60% after the hurricane. Occupancy of scrub habitat was lower than occupancy of frontal dune habitat before the hurricane (∼75% occupancy) and did not change with the hurricane. Occupancy of frontal dunes after the hurricane was influenced by percent cover of woody vegetation, dune height, and distance to nearest occupied dune. Probability of occupancy of scrub habitat was positively correlated with individual dune area and amount of surrounding dune habitat before and after the hurricane. Our study supports recent efforts to define scrub dunes as Critical Habitat for beach mice and points to the importance of enhancing dune height and reducing dune isolation in coastal restoration programs.