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Premise of the study:  We developed microsatellite (simple sequence repeat [SSR]) markers in the Neotropical tree  Handroanthus billbergii  (Bignoniaceae), to be applied in assessment of genetic diversity in this species as a reference for inferring the impact of dry forest fragmentation in Ecuador.    Methods and Results:  Using next‐generation sequencing, we detected a total of 26,893 putative SSRs reported here. Using an ABI 3500xl sequencer, we identified and characterized a set of polymorphic markers in 23 individuals belonging to three populations of  H. billbergii .    Conclusions:  We report a set of 30 useful SSR markers for  H. billbergii  and a large list of potential microsatellites for developing new markers for this or related species.

Characterization of microsatellites identified by next‐generation sequencing in the Neotropical tree Handroanthus billbergii (Bignoniaceae)