The development of a complex organ involves the specification and differentiation of diverse cell types constituting that organ. Two major cell subtypes, contractile cardial cells (CCs) and nephrocytic pericardial cells (PCs), comprise the
Drosophila
heart. Binding sites for Suppressor of Hairless [Su(H)], an integral transcription factor in the Notch signaling pathway, are enriched in the enhancers of PC-specific genes. Here we show three distinct mechanisms regulating the expression of two different PC-specific genes,
Holes in muscle
(
Him
), and
Zn finger homeodomain 1
(
zfh1
).
Him
transcription is activated in PCs in a permissive manner by Notch signaling: in the absence of Notch signaling, Su(H) forms a repressor complex with co-repressors and binds to the
Him
enhancer, repressing its transcription; upon alleviation of this repression by Notch signaling,
Him
transcription is activated. In contrast,
zfh1
is transcribed by a Notch-instructive mechanism in most PCs, where mere alleviation of repression by preventing the binding of Su(H)-co-repressor complex is not sufficient to activate transcription. Our results suggest that upon activation of Notch signaling, the Notch intracellular domain associates with Su(H) to form an activator complex that binds to the
zfh1
enhancer, and that this activator complex is necessary for bringing about
zfh1
transcription in these PCs. Finally, a third, Notch-independent mechanism activates
zfh1
transcription in the remaining,
even skipped
-expressing, PCs. Collectively, our data show how the same feature, enrichment of Su(H) binding sites in PC-specific gene enhancers, is utilized by two very distinct mechanisms, one permissive, the other instructive, to contribute to the same overall goal: the specification and differentiation of a cardiac cell subtype by activation of the pericardial gene program. Furthermore, our results demonstrate that the
zfh1
enhancer drives expression in two different domains using distinct Notch-instructive and Notch-independent mechanisms.