In molecular biology and bioinformatics, searching RNA gene occurrences in genomic sequences is a task whose importance has been renewed by the recent discovery of numerous functional RNA, often interacting with other ligands. Even if several programs exist for RNA motif search, no program exists that can represent and solve the problem of searching for occurrences of RNA motifs in interaction with other molecules. In this paper, we present a CSP formulation of this problem. We represent such RNA as structured motifs that occur on more than one sequence and which are related together by possible hybridization. Together with pattern matching algorithms, constraint satisfaction techniques have been implemented in a prototype MilPat and applied to search for tRNA and snoRNA genes on genomic sequences. Results show that these combined techniques allow to efficiently search for interacting motifs in large genomic sequences and offer a simple and extensible framework to solve such problems.