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From a single transgenic line harboring fiveTnt1transposon insertions, we generated a near‐saturated insertion population inMedicago truncatula. Using thermal asymmetric interlaced‐polymerase chain reaction followed by sequencing, we recovered 388 888 flanking sequence tags (FSTs) from 21 741 insertion lines in this population.FSTrecovery from 14Tnt1lines using the whole‐genome sequencing (WGS) and/orTnt1‐capture sequencing approaches suggests an average of 80 insertions per line, which is more than the previous estimation of 25 insertions. Analysis of the distribution pattern and preference ofTnt1insertions showed thatTnt1is overall randomly distributed throughout theM. truncatulagenome. At the chromosomal level,Tnt1insertions occurred on both arms of all chromosomes, with insertion frequency negatively correlated with theGCcontent. Based on 174 546 filteredFSTs that show exact insertion locations in theM. truncatulagenome version 4.0 (Mt4.0), 0.44Tnt1insertions occurred per kb, and 19 583 genes containedTnt1with an average of 3.43 insertions per gene. Pathway and gene ontology analyses revealed thatTnt1‐inserted genes are significantly enriched in processes associated with ‘stress’, ‘transport’, ‘signaling’ and ‘stimulus response’. Surprisingly, gene groups with higher methylation frequency were more frequently targeted for insertion. Analysis of 19 583Tnt1‐inserted genes revealed that 59% (1265) of 2144 transcription factors, 63% (765) of 1216 receptor kinases and 56% (343) of 616 nucleotide‐binding site‐leucine‐rich repeat genes harbored at least oneTnt1insertion, compared with the overall 38% ofTnt1‐inserted genes out of 50 894 annotated genes in the genome.