In total, 288 slimy sculpins, Cottus cognatus, were collected in September 2003 from 6 Lake Michigan, U.S.A., ports, along with 220 ninespine sticklebacks, Pungitius pungitius, from 3 ports. The ports included Waukegan, Illinois; Port Washington (PW) and Sturgeon Bay (SB), Wisconsin; and Manistique (MS), Frankfort (FF), Ludington (LD), and Saugatuck, Michigan. Echinorhynchus salmonis infected sculpins from 6 ports, Acanthocephalus dirus infected sculpins from 4 ports, and Neoechinorhynchus pungitius infected sculpins from 3 ports. Echinorhynchus salmonis infected significantly more sculpins at PW and at FF than at MS and LD. There were several significant differences in the intensities and abundances of E. salmonis among ports. Acanthocephalus dirus significantly infected more sculpins and had significantly higher abundances at FF than at PW, MS, and LD. Echinorhynchus salmonis, A. dirus, and N. pungitius infected sticklebacks from SB, MS, and FF. Neoechinorhynchus pungitius significantly infected more sculpins and more sticklebacks, and it had significantly higher abundances at MS than at FF. Neoechinorhynchus pungitius was the most common acanthocephalan in C. cognatus and P. pungitius at MS. These acanthocephalan species infecting C. cognatus and P. pungitius corresponded in their occurrence to those organisms that serve as their intermediate hosts found in the stomachs of both fish species. Potential changes in the diet of C. cognatus played a role in significant differences found for E. salmonis and N. pungitius at MS. One of these acanthocephalan species was always the most numerous helminth species found in the digestive tracts of P. pungitius and C. cognatus from these Lake Michigan ports.