MADS-box transcription factors possess many functions in plant reproduction and development. However, few MADS-box genes related to secondary metabolites regulation have been identified. In
H
evea
brasiliensis
, natural rubber is a representative
cis
-polyisoprenoids in secondary metabolism which occurs in the rubber laticifer cells, the molecular regulation basis of natural rubber biosynthesis is not clear. Here, a total of 24 MADS-box genes including 4 type I MADS-box genes and 20 type II MADS-box genes were identified in the transcriptome of rubber tree latex. The phylogenetic analysis was performed to clarify the evolutionary relationships of all the 24 rubber tree MADS-box proteins with MADS-box transcription factors from
Arabidopsis thaliana
and
Oryza sativa
. Four type I MADS-box genes were subdivided into Mα (3 genes) and Mβ (1 gene). Twenty type II MADS-box genes were subclassified into MIKC* (8 genes) and MIKC
c
(12 genes). Eight MADS-box genes (
HblMADS3
,
5
,
6
,
7
,
9
,
13
,
23
,
24
) were predominant expression in laticifers. ABA up-regulated the expression of
HblMADS9
, and the expression of
HblMADS3
,
HblMADS5
,
HblMADS24
were up-regulated by MeJA. The function of HblMADS24 was elucidated. HblMADS24 bound
HbFPS1
promoter in yeast and HblMADS24 activated
HbFPS1
promoter in tobacco plants. Moreover, we proposed that HblMADS24 is a transcription activator of
HbFPS1
which taking part in natural rubber biosynthesis.