The genetic diversity and population abundance of penaeid shrimps were studied based on morphometric length–weight relationships during monsoon seasons in 2011 from Malindi–Ungwana Bay with southeast monsoon (SEM) being cooler than northeast monsoon (NEM). A total of 1364 penaeid shrimps were randomly collected from the four main artisanal fishing areas in the estuaries and two other areas within the shallow waters trawling grounds. Fenneropenaeus indicus was most abundant species with a relative proportion of 30.8%, followed by Metapenaeus monoceros (24.9%), Penaeus semisulcatus (15.2%), Marsupenaeus japonicus (10.3%), Penaeus monodon (9.7%) and Penaeus canaliculatus (0.9%). This study showed higher shrimp abundance during SEM compared to NEM season despite its proportional decrease with increasing water depths. The overall combined sex ratio deviated from the expected ratio of 1:1 (p < 0.05) with females dominating the total catch (1 male: 1.50 female), while most penaeid species exhibited positive allometric growth significantly different from 3.0 (p < 0.05) with strong relationship between lengths and weights of these species. The carapace length of six penaeid shrimps at first maturity (L50) suggested that their spawning starts at different sizes. Following good condition factors and high abundance of M. monoceros and F. indicus with matured gonads in both seasons, this study confirmed the two species for shrimp mariculture breeding programmes in Kenya. Generally, high variability among individual shrimps within each population indicated the presence of high genetic diversity in Malindi–Ungwana Bay. This study, therefore, recommends conservation measures to prevent growth overfishing in the estuarine area
