Abstract
Waterlogging (WL) has emerged as a serious threat for chilli (
Capsicum annuum
L.) growth and productivity. A practical approach to overcome this challenge is to explore chilli germplasms with enhanced tolerance to WL stress. This study investigated the responses of 12 diverse chilli genotypes to short‐term WL stress and subsequent recovery at the seedling stage. The 35‐d‐old chilli seedlings were exposed to three growth conditions in pots: (i) control (no stress), (ii) WL (3‐d), and (iii) recovery (6‐d after WL), following a completely randomized design with three replications. WL stress significantly declined root‐shoot biomass, pigment contents, stomatal conductance (
g
s
), transpiration rate (
E
), quantum yield of PSII (
Φ
P
S
I
I
), and electron transport rate (ETR) while markedly increased malondialdehyde (MDA), hydrogen peroxide (H
2
O
2
), proline contents, and total antioxidant capacity (TAC) in all tested genotypes. The genotypes varied significantly in response to the studied traits demonstrating tolerance and susceptibility. Depending on genotypes, total dry weight was reduced by 16%–36% under WL compared to control while only 8%–16% of the lost dry weight was recovered after a six‐day recovery. WL triggered severe impact on
g
s
, reducing by 75%–95% across the genotypes compared to control. WL boosted leaf MDA by 30% in Sariakandi‐1 to 60% in BARI Morich‐3 compared to control, while after recovery, MDA levels decreased by 9%, 12%, and 15% in Premium, Current, and Sariakandi‐1, respectively. Under WL, the leaf proline and TAC in Current, Premium, and SK‐1 boosted by 72%, 80% and 82% and by 78%, 82%, and 83%, respectively, compared to control. Based on stress tolerance index (STI) of all measured traits, hierarchical clustering ranked Sariakandi‐1, Premium, BARI Morich‐5, and Current as relatively more tolerant to WL with comparatively better but partial recovery through the restoration of morpho‐physiological and biochemical attributes. Principal component analysis identified key traits as potential selection criteria for breeding WL‐tolerant chilli cultivars.