Using data from our annual lakewide bottom trawl survey of Lake Michigan, we calculated the mean depths of capture for deepwater sculpin Myoxocephalus thompsonii and slimy sculpin Cottus cognatus for each combination of transect (Frankfort, Ludington, Saugatuck, and Manistique in Michigan, Waukegan in Illinois, and Port Washington and Sturgeon Bay in Wisconsin) and year (1973-2005). The mean depth of capture of both sculpin species significantly decreased during the recovery phase of the deepwater sculpin population at four of the transects but did not significantly change for either species at the other three transects during this time. During the postrecovery phase of the deepwater sculpin population, the mean depth of capture of deepwater sculpins significantly increased at six of the seven transects, whereas that for slimy sculpins significantly increased at only four of the seven transects. The mean depth of capture of deepwater sculpins was most strongly correlated with that of slimy sculpins at Frankfort (r = 0.73); the correlation was weakest at Manistique (r = 0.00). Long-term mean depths of capture (averaged over all years) for deepwater sculpins ranged from 90 to 108 m among the seven transects, whereas the long-term mean depths of capture for slimy sculpins ranged from 60 to 83 m. The long-term mean depth difference between the two species was least at Frankfort (21 m) and greatest at Manistique (38 m); at all seven transects, the mean depth difference was significantly greater than zero. We concluded that these two sculpin populations in Lake Michigan maintained some degree of spatial separation during 1973-2005.