FLORICAULA/LEAFY (FLO/LFY) is a single-copy nuclear-encoded homeotic gene containing two introns. We have investigated the utility of the second intron of FLO/LFY (FLint2) as a tool for phylogeny reconstruction at lower taxonomic levels. As an example, the phylogeny of 46 Amorphophallus, two Pseudodracontium, and four outgroup species is reconstructed using maximum parsimony and maximum likelihood analyses of FLint2 sequences. We designed new primers based on conserved sequences of the second and third exon for use in a range of Aroid taxa to amplify and sequence the second intron. In Amorphophallus FLint2 proved to be rather short (143-222 bp), highly variable and unsaturated. In all but two species a single amplification product was found. Results from phylogenetic analysis of FLint2 are largely congruent with results using the chloroplast regions rbcL, matK, and trnL, and compare favorably in percentage of informative characters, overall homoplasy levels, number of well-supported clades in consensus trees and resolution of ingroup relationships within Amorphophallus. When amplification products are not too large, alignment is relatively straightforward, and sequences are used in combination with other fast evolving markers, the FLint2 intron may be a valuable new tool for phylogenetic studies at lower taxonomic levels.