Interest in greenhouse system of cultivation is on the increase among pepper farmers in southwest Nigeria however, little is known about how to maximize yield using the right fertilizer and water combination. This experiment therefore assessed the effects of fertigation regimes on the growth, yield and resource-use efficiency of greenhouse-grown pepper species in a rainforest zone of Nigeria.  A 3 by 2 by 2 factorial experiment was conducted using three nitrogen fertilizer rates (0, 60 and 100 kgN/ha), irrigation regimes at 100 and 70% field capacity and Capsicum species (habanero: Capsicum sinensis L.) and bell pepper: Capsicum annuum L.)  laid out in a split-split plot design with four replications. Results showed that irrigation application at 70 % field capacity combined with 60 kgN/ha enhanced pepper growth, fruit yield characters and water and nutrient use efficiencies. Habanero species out-performed sweet pepper under greenhouse conditions. Irrigation application at 100 % FC and nitrogen (100 kgN/ha) did not significantly improve yield or resource efficiency compared with 70 % FC and 60 kgN/ha. Thus, findings from the study suggest that moderate fertigation regime is optimal for growth, yield and resource-use efficiency of pepper. Habanero pepper produced higher fruit yield and utilized nutrient and water more efficiently compared with bell pepper. It is therefore recommended that fertilizer rate of 60 kgN/ha, coupled with irrigation at 70 % field capacity be adopted as a strategy for greenhouse pepper cultivation in the rainforest environment of Nigeria.