This study presents a simple but highly versatile method of fabricating picoliter-volume hydrogel patterns on poly(dimethylsiloxane) (PDMS) substrates. Hydrophilic regions were prepared on hydrophobic PDMS plates by trapping and melting functional polymer particles and performing subsequent reactions with partially oxidized dextran. Small aliquots of a gelation solution were selectively trapped on the hydrophilic areas by a simple dipping process that was utilized to make thin hydrogel patterns by the in situ gelation of a sol solution. Using this process, we successfully formed calcium alginate, collagen I, and chitosan hydrogels with a thickness of several micrometers and shapes that followed the hydrophilized regions. In addition, alginate and collagen gel patterns were used to capture cells with different adhesion properties selectively on or off the hydrogel structures. The presented strategy could be applicable to the preparation of a variety of hydrogels for the development of functional biosensors, bioreactors, and cell cultivation platforms.