The marine microscopic jaw worms, Gnathostomulida, belong to the early branching spiralian lineage Gnathifera and consist of two main clades—Filospermoidea and Bursovaginoidea. Previous studies of gnathostomulid musculature focused on the bursovaginoid taxa, and only LM and TEM techniques were employed in the previous investigations of two filospermoids, Haplognathia simplex and Pterognathia swedmarki. In the present study, we used F-actin staining combined with CLSM to reconstruct the musculature of H. simplex and H. filum and found far-reaching similarities in their jaw musculature. In addition to known pharyngeal muscles we found new apophyseal abductors not uncovered in bursovaginoid gnathostomulids, but which resemble certain muscles of the sister group (Micrognathozoa + Rotifera) and may present an autapomorphy of Gnathifera. The body wall musculature exhibits greater interspecific variation: H. simplex possesses a simple grid of thick longitudinal and thin circular muscles, whereas H. filum shows a very sparse body wall musculature devoid of circular fibers, a pattern similar to another interstitial worm, the enigmatic annelid Lobatocerebrum. The flexibility gained hereby may similarly represent an adaptation and restriction to ciliary gliding among sand grains.