This study aim to investigate the morphological and genetic characterization of strains of Clariid fish species in some river bodies in Kano Stateusing microsatellite markers.One hundred and seventy seven Clariid fish samples (Clariasgariepinus and Heterobranchuslongifilis)were collected from six rivers (Thomas, Ghari, Tiga dam, Duddurun Gaya, Karaye and Bagwai) in Kano state. Body weight, twenty-two morphometric characteristics and four meristic counts were measured on each fish sample to determine the influence of river location, strain of fish and sex.Body weight was measured in grams using sensory scale, the morphometric measurements were measured in centimetres using flexible tapewhile meristic counts were counted visually.The morphometric characteristics taken on the body were; Body weight (BW), Total length (TL), Standard length (SL), Pre-dorsal distance (PDD), Pre-anal distance (PAD), Pre-ventral distance (PVD), Pre-pectoral distance (PPD),Caudal peduncle depth (CPD), Body depth at anus (BDA); measurements taken on the fin were; Dorsal fin length (DFL), Anal fin length (AFL), Pectoral fin length (PFL), Pectoral spine length (PSL); measurements taken on the head region were;Dorso-caudal length (DDCF), Dorso-occipital length (DODF), Head length (HL), Head width (HW), Snout length (SNL), Inter-orbital distance (ID), Eye diameter (ED), Length of occipital fontanelle (OFL), Width of occipital fontanelle (OFW) and Snout-occipital length (DSO). The meristic counts were; Dorsal fin ray count (DFRC), Pectoral fin ray count (PFRC), Anal fin ray count (AFRC) and Caudal fin ray count (CFRC).The total length (TL) and body weight (BW) of each fish sample was used to compute Length-Weight relationships using the formula: W = log a + b log L and K = 100W/L3 was used to compute Condition Factor. Blood sample was taken from each fishsampleby severing the caudal peduncle and drained into FTA cards for DNA extraction, Polymerase Chain Reaction and electrophoresis to determine genetic variationbetween the Clariid fish populations. Data gotten from the morphometric measurements were analysed appropriately using GLM procedures of SAS 9.4 to show the influence of river location, strain, and sex, Duncan multiple range test was used for mean separation, Principal component analysis of SPSS was used for possible data reduction, and Genealex 6.4 software package was used to analyse the resolve bands from DNA extraction to determine their base pair and genetic variation. Body weight, morphometric measurements and meristic countswere significantly affected (P<0.01,0.05) by location and strain while sex had effect (P<0.01, 0.05) only on total length, standard length, dorsal fin length, dorso-caudal length, caudal peduncle depth, anal fin length, head length, inter-orbital distance, eye diameter and length of occipital fontanelle. The equation for the length-weight relationship for the three strains were: C. gariepinus = -329.86+17.56TL andH. longifilis= -241.49+14.28TL.The condition factors showed varying degree of wellbeing of fish samples in their habitat (K = 0.37 to 0.89). Tiga dam had the best condition factor (0.81-0.89) followed by fishes caught in River Ghari (0.74-0.88). Pearson correlation analysis for all the variables measured showed that relationship between Body Weight and all the morphometric measurements were positive and significant. The â€-r' values ranged from low (0.23) to high (0.80) for BW/PDD and BW/DDCF. The other measurements had positive and significant relationships with values ranging from 0.30 for ED/SL to 0.92 for TL/SL. Principal component analysis indicated that most of the variables could be used for discrimination with regard to the species with a total variance of 82.52% shared as 47.66%, 19.16%, 8.67% and 7.03% for PC1, PC2, PC3 and PC4, respectively. Among the populations sampled, the genetic similarity ranged from 0.018 to 0.079 whilethe genetic distance ranged from 0.112 to 0.998. The Fst values ranged from 0.000 to 0.663, Fit ranged from -0.041 to 0.115, Fis ranged from -0.350 to -0.262. The result indicated a large number of gene flow (exchange) among the populations with a range of 0.455 to 0.866. The populations were not genetically pure but heterogeneous with varying degrees of genetic similarity and distance. Since there was no inbreeding as shown in the study, none of the population exhibited genetic uniqueness. The populations had a high genetic differentiation between populations but moderate differentiation within populations. The populations were outbred populations; an indication that relatives avoided mating in the population. There was an established magnitude of genetic divergence (91.86%) among the populations as shown by the result of the percentage polymorphism which depends on the number of alleles detected per locus and their frequencies. The study indicated that river location and species of fish had a significant influence on Clariid fish morphometric measurements and meristic counts. The study also gave an indication that the growth pattern of Clariid species in Kano State Rivers was positive allometric growth pattern (b>3) and the Clariid fishes are in good condition of wellbeing as indicated in the condition factor.