Alternating light-dark laminae within stromatolites have been attributed to a phototactic response of the constituent microbial communities, whereby filaments orient vertically during the day and recline at night. This study examines the orientation of cyanobacterial filaments within a laminated siliceous stromatolite from a Yellowstone National Park hot spring to identify the controls on microfabric development and whether phototaxis plays a role. Results indicate that filament orientation is predominantly perpendicular or parallel to lamination, even when laminae are steeply inclined. Thus, phototaxis is not a significant control of microfabric development in these stromatolites. Vertical aspects of the fabric are dominated by hourglass-shaped filament bundles (hourglass structures) adjacent to rounded pores, rather than being defined by individual filaments. The rounded pores likely represent oxygen-rich bubbles generated during photosynthesis. Upon stabilization by filaments, upward buoyancy of the bubbles rotated the bundles toward a vertical orientation. Thus, vertical aspects of the fabric in this stromatolite result from buoyancy forces rather than phototaxis. Examples from the Neoproterozoic Beck Spring Dolomite reveal that similar subvertical hourglass structures are present in the rock record and may be better preserved than individual filaments. The presence of rounded pores (fenestrae) and hourglass structures in ancient microbialites, here termed the hourglass-associated fenestral fabric, can serve as an indication of biogenic influence in stromatolites, especially in the absence of preserved filaments, and may be an indication of oxygenic photosynthesis.