Abstract In reproductive technologies, uncovering the molecular aspects of oocyte and embryo competence under different conditions is crucial for refining protocols and enhancing efficiency. RNA-seq generates high-throughput data and provides transcriptomes that can undergo additional computational analyses. This study presented the transcriptomic profiles of in vitro matured oocytes and blastocysts produced in vitro from buffalo crossbred (Bubalus bubalis), coupled with gene co-expression and module preservation analysis. Cumulus Oophorus Complexes, obtained from slaughterhouse-derived ovaries, were subjected to in vitro maturation to yield metaphase II oocytes (616) or followed in vitro fertilization and culture to yield blastocysts for sequencing (526). Oocyte maturation (72%, ±3.34 sd) and embryo development (21.3%, ±4.18 sd) rates were obtained from three in vitro embryo production routines following standard protocols. Sequencing of 410 metaphase II oocytes and 70 hatched blastocysts (grade 1 and 2) identified a total of 13,976 genes, with 62% being ubiquitously expressed (8,649). Among them, the differentially expressed genes (4,153) and the strongly variable genes with the higher expression (fold-change above 11) were highlighted in oocytes (BMP15, UCHL1, WEE1, NLRPs, KPNA7, ZP2, and ZP4) and blastocysts (APOA1, KRT18, ANXA2, S100A14, SLC34A2, PRSS8 and ANXA2) as representative indicators of molecular quality. Additionally, genes exclusively found in oocytes (224) and blastocysts (2,200) with specific biological functions were identified. Gene co-expression network and module preservation analysis revealed strong preservation of functional modules related to exosome components, steroid metabolism, cell proliferation, and morphogenesis. However, cell cycle and amino acid transport modules exhibited weak preservation, which may reflect differences in embryo development kinetics and the activation of cell signaling pathways between buffalo and bovine. This comprehensive transcriptomic profile serves as a valuable resource for assessing the molecular quality of buffalo oocytes and embryos in future in vitro embryo production assays. technologies efficiency RNAseq RNA seq highthroughput high throughput analyses Bubalus bubalis, bubalis , bubalis) coexpression co Complexes slaughterhousederived slaughterhouse derived ovaries 616 (616 526. 526 . (526) 72%, 72 (72% 334 3 34 ±3.3 sd 21.3%, 213 21 (21.3% 418 4 18 ±4.1 41 7 grade 2 13976 13 976 13,97 62 8,649. 8649 8,649 8 649 (8,649) them 4,153 4153 153 (4,153 foldchange fold change 11 BMP15, BMP15 BMP (BMP15 UCHL1 UCHL WEE1 WEE NLRPs KPNA7 KPNA ZP2 ZP ZP4 APOA1, APOA1 APOA (APOA1 KRT18 KRT ANXA2 ANXA S100A14 SA S A SLC34A2 SLCA SLC PRSS Additionally 224 (224 2,200 2200 200 (2,200 components metabolism proliferation morphogenesis However bovine assays 61 (61 52 (526 72% (72 33 ±3. 21.3% (21.3 ±4. 1397 97 13,9 6 864 8,64 64 (8,649 4,15 415 15 (4,15 BMP1 (BMP1 (APOA KRT1 S100A1 SLC34A 22 (22 2,20 220 20 (2,20 (6 5 (52 (7 ±3 21.3 (21. ±4 139 9 13, 86 8,6 (8,64 4,1 (4,1 (BMP S100A (2 2,2 (2,2 ( (5 ± 21. (21 8, (8,6 4, (4, 2, (2, (8, (4 (8