Oreochromis species are of economic importance in fisheries and aquaculture but threatened by human‐mediated activities. Effective conservation and their sustainable management require genetic monitoring tools that can assess genetic variation across species. Various neutral markers have been used to monitor biodiversity in organisms, but they are limited in cross‐amplification among various taxa. Non‐neutral markers such as Exon‐Primed Intron Crossing (EPIC) not only cross amplify various taxa but also target gene regions that are likely to be involved in adaptive responses to selective pressure. This study therefore developed 50 EPIC markers from Oreochromis niloticus reference genome targeting immune related genes to assess their potential to cross‐amplify Oreochromis species. Genetic diversity, population structure, and differentiation was measured among Oreochromis niloticus , O. jipe , O. esculentus and O. leucostictius species and their respective populations from eleven African water bodies and two aquaculture farms. 45 EPIC markers successfully amplified target regions across the four Oreochromis species. O. niloticus exhibited the highest diversity (He = 0.50), followed by O. jipe (He = 0.29), O. leucostictus (He =0.28) and O. esculentus with the lowest (He = 0.25). The highest differentiation values were observed among populations of different species while the lowest was among farmed O. niloticus . This was supported by AMOVA results that showed highest genetic differentiation among species. Population structure analyses were concordant with species boundaries while showing detailed intraspecific clustering patterns among the O. niloticus populations that reflected geographical origin. The observed genetic diversity, gene flow, and population differentiation confirms the applicability of EPIC markers as molecular tools for monitoring biodiversity and guiding the conservation of Oreochromis species under increasing anthropogenic and environmental pressures.

Despite ongoing biosecurity and control efforts, aquaculture intensification in the Lake Victoria Crescent has led to a persistent increase in parasitic disease occurrence in cultured Nile tilapia. Notably, different culture systems provide different habitats and environmental conditions for parasites and understanding these dynamics may provide better management strategies. We compared parasitic infection/infestation rates of cultured Nile tilapia in pond-based and cage-based farming systems and identified associations between parasite dynamics and management in the Crescent. Trichodina spp. (most prevalent and abundant) and Cichlidogyrus spp. were found in all systems. Pond systems contained ≥11 parasitic genera while ≤5 were found in cage systems. Parasite dynamics were modelled using generalised linear models with zero-inflated Poisson or zero-inflated negative binomial distributions. Surprisingly, in pond systems, adequate stocking densities and feeding were associated with an increase in Cichlidogyrus spp. abundance, while sourcing seed from fellow fish farmers was associated with a decrease in Trichodina spp abundance. For cage systems, adequate stocking densities and feeding were associated with an increase in Trichodina spp. abundance. Wild fish entry was associated with an increase in Cichlidogyrus spp. abundance while optimal stocking density was associated with a decrease in Cichlidogyrus spp. abundance. These findings highlight the interactions between seasonality and farm management in the control of parasites.

With increasing aquaculture intensification, emergence of fish ill-health incidents is expected, particularly under hatchery conditions, owing to stress attributed to for instance poor water quality and overcrowding, and improper nutrition. The objective of this study was to explore the ill-health incidents in fish hatcheries in Uganda. This was done using a face-to-face interview using a semi-structured questionnaire. A total of 48% of the 56 sampled hatcheries had experienced fish disease incidents, with African catfish being the most affected species (81.5%). Disease signs and symptoms were mainly observed during the fry (66.7%), fingerling (55.6%) and larva (51.9%) stages. Among 27 hatcheries, the most common disease signs and symptoms observed were cotton-wool growth (20), red spots on skin and fins (12), fish swimming upside down (12), and tail and fin rot (11). The analysis revealed that the level of experience of the farmer, the type of hatchery facility, and water quality monitoring were significantly associated with ill-health incidents in hatcheries. The results inform policy and practice, improving disease prevention and control to safeguard fish health and ensure Uganda’s long-term viability aquaculture.

Aquaculture is a key to global food and nutrition security, but intensification has increased disease pressure, antibiotic use, antimicrobial resistance (AMR), and wider One Health concerns. Functional microbial products (FMPs), including probiotics, prebiotics, synbiotics, postbiotics, and paraprobiotics, are widely promoted as sustainable alternatives to antibiotics. However, their growing use has not resulted in sustained replacement of antibiotics in commercial aquaculture practice. This review examined why this gap persists and what conditions are required for these products to contribute credibly to antibiotic reduction. A PRISMA‐guided systematic review was conducted across major scientific databases, yielding 654 records, of which 97 studies were retained for qualitative synthesis. The evidence shows that FMPs can improve growth, feed efficiency, immune response, disease resistance, survival, and, in some systems, water quality. Beyond these performance outcomes, the review identifies host immune modulation as a central biological pathway linking FMPs to disease resilience, particularly through mucosal barrier reinforcement, innate immune priming, activation of humoral and cellular defenses, cytokine and inflammatory regulation, antioxidant protection, and stabilization of the host–microbiome axis. Probiotics had the strongest overall evidence base, synbiotics showed the most consistent combined gains across growth, immunity, and survival, while postbiotics emerged as promising options because of their stability and biosafety advantages. However, direct evidence of sustained farm‐level reductions in antibiotic use remains limited. Multiple interlinked constraints explain this gap including biophysical stress in production systems, inconsistent product quality, misaligned application practices, mechanistic uncertainty, biosafety risk, and weak diagnostic, advisory, and regulatory systems. Overall, FMPs are best understood as preventive and resilience‐building tools rather than direct therapeutic substitutes for antibiotics. Meaningful antibiotic reduction will depend less on product substitution alone and more on integrating these products into stronger health‐management systems supported by quality control (QC), clear deployment protocols, diagnostics, advisory services, and enabling regulation.