Neohesperidosides are disaccharides that are present in some flavonoids and impart a bitter taste, which can significantly affect the commercial value of citrus fruits. In this study, we identified three flavonoid-7-
O
-
di
-glucosyltransferase (
dGlcT
) genes closely related to 1,2-rhamnosyltransferase (
1,2RhaT
) in citrus genomes. However, only
1,2RhaT
was directly linked to the accumulation of neohesperidoside, as demonstrated by association analysis of 50 accessions and co-segregation analysis of an F
1
population derived from
Citrus reticulata
×
Poncirus trifoliata
. In transgenic tobacco BY2 cells, over-expression of
CitdGlcT
s resulted in flavonoid-7-
O
-glucosides being catalysed into bitterless flavonoid-7-
O
-
di
-glucosides, whereas over-expression of
Cit1,2RhaT
converted the same substrate into bitter-tasting flavonoid-7-
O
-neohesperidoside. Unlike
1,2RhaT
, during citrus fruit development the
dGlcT
s showed an opposite expression pattern to
CHS
and
CHI
, two genes encoding rate-limiting enzymes of flavonoid biosynthesis. An uncoupled availability of dGlcTs and substrates might result in trace accumulation of flavonoid-7-
O
-
di
-glucosides in the fruit of
C. maxima
(pummelo). Past human selection of the deletion and functional mutation of
1,2RhaT
has led step-by-step to the evolution of the flavor-related metabolic network in citrus. Our research provides the basis for potentially improving the taste in citrus fruit through manipulation of the network by knocking-out
1,2RhaT
or by enhancing the expression of
dGlcT
using genetic transformation.