Phormidium, a genus of filamentous cyanobacteria, forms endosymbiotic associations with seedling roots that accelerate the growth of the vegetable seedlings. Understanding the gliding mechanism of Phormidium will facilitate improved formation of this association and increased vegetable production. To observe the gliding movements, we fabricated various microfluidic chips termed nanoaquariums using a femtosecond (fs) laser. Direct fs laser writing, followed by annealing and successive wet etching in dilute hydrofluoric acid solution, can easily produce three-dimensional (3D) microfluidics with different structures embedded in a photostructurable glass. Using the fs laser, optical waveguides and filters were integrated with the microfluidic structures in the microchips, allowing the gliding mechanism to be more easily clarified. Using this apparatus, we found that CO(2) secreted from the seedling root attracts Phormidium in the presence of light, and determined the light intensity and specific wavelength necessary for gliding.